Contacts of the helix formed by residues 93 - 113 (chain K) in PDB entry 4ZZ7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 93 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K LYS* 1.3 76.6 - - - +
94K ALA* 1.3 74.4 + - + +
95K HIS* 3.3 32.1 - - + +
96K ASP* 2.9 19.6 + - - +
97K ALA* 3.1 8.5 + - - -
311K GLY 4.3 6.5 - - - +
313K SER* 4.0 18.8 - - - +
315K ASP 4.8 0.7 - - - +
316K SER* 3.6 15.7 - - - +
317K GLY 3.5 21.8 - - - +
318K ASN* 3.3 36.3 - - + +
319K ASP 4.9 0.2 - - - +
320K PHE* 3.9 27.1 - - - +
321K GLY* 4.0 2.9 - - - +
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Residues in contact with ALA 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K CYS* 4.3 9.5 - - + -
92K LYS 4.0 0.6 + - - -
93K ILE* 1.3 75.1 - - + +
95K HIS* 1.3 59.0 + - - +
97K ALA* 3.1 7.4 + - - +
98K MET* 2.8 37.7 + - + +
313K SER* 5.0 4.8 + - - +
316K SER* 3.7 21.7 + - - +
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Residues in contact with HIS 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93K ILE* 3.0 35.1 + - + +
94K ALA* 1.3 79.4 - - - +
96K ASP* 1.3 86.7 + - - +
98K MET* 3.8 6.5 - - - +
99K GLY* 3.0 24.8 + - - -
317K GLY* 5.5 0.8 + - - -
318K ASN 3.4 13.2 - - - -
319K ASP* 3.3 21.7 + - - -
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Residues in contact with ASP 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K LYS* 3.9 19.0 + - + +
93K ILE 2.9 11.6 + - - +
95K HIS* 1.3 103.5 + - - +
97K ALA* 1.3 59.0 + - - +
99K GLY* 3.4 2.4 + - - -
100K GLU* 3.0 27.2 + - - +
274K GLY* 4.9 2.3 - - - -
275K SER* 3.2 46.4 + - - +
279K ARG* 4.2 6.9 + - - -
319K ASP 4.0 6.8 - - - +
320K PHE* 4.6 4.3 - - - -
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Residues in contact with ALA 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K CYS* 3.4 29.2 - - + +
86K ILE* 3.9 29.9 - - + +
92K LYS* 3.8 11.4 - - + +
93K ILE 3.1 8.7 + - - +
94K ALA* 3.1 8.6 + - - +
96K ASP* 1.3 76.8 - - - +
98K MET* 1.3 60.0 + - - +
100K GLU* 3.3 4.0 + - - +
101K LEU* 2.9 28.8 + - - +
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Residues in contact with MET 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K ALA* 4.1 24.2 - - + +
80K ASP* 5.5 4.5 - - - +
83K CYS* 3.2 23.3 - - + -
94K ALA* 2.8 23.7 + - + +
95K HIS* 3.8 7.2 - - - +
97K ALA* 1.3 68.1 - - - +
99K GLY* 1.3 55.9 + - - +
101K LEU* 3.2 8.4 + - + +
102K GLN* 2.7 53.3 + - + +
105K ILE* 6.3 0.9 - - + -
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Residues in contact with GLY 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K HIS 3.0 18.8 + - - -
96K ASP 3.8 1.8 - - - -
97K ALA 3.4 0.2 - - - -
98K MET* 1.3 74.9 - - - +
100K GLU* 1.3 61.3 + - - +
102K GLN* 3.3 6.6 + - - +
103K ARG* 3.1 34.6 + - - +
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Residues in contact with GLU 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K ILE* 4.0 7.2 - - - +
92K LYS* 2.9 29.8 + - - +
96K ASP 3.0 13.0 + - - +
97K ALA 3.4 7.6 - - - +
98K MET 3.2 0.2 - - - -
99K GLY* 1.3 73.6 - - - +
101K LEU* 1.3 60.4 + - - +
103K ARG* 3.3 6.5 + - - +
104K GLY* 2.9 23.9 + - - -
150K PHE* 3.1 30.0 - - + -
151K PRO* 3.2 7.8 - - - +
152K VAL* 2.7 36.9 + - + -
153K MET* 2.9 30.8 + - + +
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Residues in contact with LEU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75K LEU* 3.8 16.2 - - + +
79K ALA* 3.5 45.3 - - + +
82K ILE* 4.0 26.5 - - + -
83K CYS* 4.5 6.3 - - - -
86K ILE* 5.4 0.4 - - + -
97K ALA 2.9 16.4 + - - +
98K MET* 3.6 11.0 - - + +
100K GLU* 1.3 76.5 - - - +
102K GLN* 1.3 56.3 + - - +
104K GLY* 3.3 1.2 + - - -
105K ILE* 2.9 49.7 + - + +
152K VAL* 3.8 27.1 - - + +
156K LEU* 5.0 1.8 - - + -
184K ILE* 5.2 0.2 - - + -
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Residues in contact with GLN 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ARG* 4.0 29.2 - - - +
76K GLU* 5.4 4.1 + - - +
98K MET* 2.7 35.3 + - + +
99K GLY* 3.5 8.7 - - - +
100K GLU 3.2 0.2 - - - -
101K LEU* 1.3 73.6 - - - +
103K ARG* 1.3 59.2 + - + +
105K ILE* 3.1 24.5 + - - +
106K GLU* 3.0 38.7 + - - +
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Residues in contact with ARG 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K GLY 3.1 21.3 + - - +
100K GLU* 3.8 1.2 - - - +
102K GLN* 1.3 74.1 - - + +
104K GLY* 1.3 63.5 + - - +
106K GLU* 3.3 22.2 + - - +
107K ASN* 2.9 26.8 + - - +
150K PHE* 4.6 12.7 - - - -
153K MET* 3.2 47.7 - - - +
157K TRP* 5.3 0.4 - - - -
279K ARG* 5.9 2.8 - - - +
440K LEU* 6.3 1.0 - - - +
442K VAL* 3.7 41.8 - - - +
443K PRO 5.4 2.7 + - - -
444K VAL* 6.6 0.2 - - - +
445K ALA* 5.2 0.2 - - - +
449K PHE* 5.9 0.6 - - - -
463K TYR* 5.7 0.2 + - - -
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Residues in contact with GLY 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K GLU 2.9 14.3 + - - -
101K LEU 3.6 2.7 - - - -
102K GLN 3.2 0.2 - - - -
103K ARG* 1.3 75.8 - - - +
105K ILE* 1.3 63.9 + - - +
107K ASN* 3.2 20.9 + - - +
108K VAL* 3.3 15.2 + - - +
153K MET* 4.2 6.9 - - - +
156K LEU* 3.6 30.0 - - - +
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Residues in contact with ILE 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K LYS* 3.8 28.9 - - + -
75K LEU* 3.9 25.4 - - + -
76K GLU* 3.9 30.3 - - + +
98K MET* 6.3 1.3 - - + -
101K LEU* 2.9 40.9 + - + +
102K GLN* 3.1 23.3 + - - +
104K GLY* 1.3 74.2 - - - +
106K GLU* 1.3 52.2 + - - +
108K VAL* 2.8 13.5 + - - +
109K GLU* 2.8 42.4 + - - +
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Residues in contact with GLU 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I LEU* 4.2 15.9 - - + +
66I ARG* 3.7 20.8 + - - +
102K GLN* 3.0 26.3 + - - +
103K ARG* 3.4 26.5 - - - +
105K ILE* 1.3 77.0 - - - +
107K ASN* 1.3 55.3 + - - +
109K GLU* 3.2 23.0 + - - +
110K TYR 3.0 23.9 + - - -
444K VAL* 3.7 21.8 - - - +
445K ALA* 3.2 22.3 + - + +
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Residues in contact with ASN 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ARG* 2.9 18.7 - - - +
104K GLY* 3.2 12.3 + - - +
105K ILE 3.2 0.4 - - - -
106K GLU* 1.3 75.8 - - - +
108K VAL* 1.3 60.8 + - - +
110K TYR* 3.6 5.2 + - - +
111K ALA* 3.3 20.6 + - - +
156K LEU 3.1 25.2 - - - +
157K TRP* 3.3 22.5 + - - +
160K PRO* 4.4 3.5 - - - +
161K MET* 5.3 2.6 + - - +
445K ALA* 3.9 11.9 + - - +
463K TYR* 3.4 43.4 - - + +
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Residues in contact with VAL 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K MET* 3.3 43.9 - - + +
71K PHE* 3.9 17.5 - - + -
72K LYS* 4.0 14.1 - - + +
75K LEU* 3.8 23.1 - - + -
104K GLY 3.4 14.6 - - - +
105K ILE* 2.8 11.3 + - - +
107K ASN* 1.3 75.6 - - - +
109K GLU* 1.3 62.4 + - - +
111K ALA* 3.0 17.3 + - - +
112K CYS* 3.1 13.2 + - - -
156K LEU* 4.1 7.6 - - + -
160K PRO* 4.4 3.8 - - + -
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Residues in contact with GLU 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I LEU* 3.4 21.0 - - + +
66I ARG* 2.6 36.4 + - - -
69I PHE* 3.9 24.4 - - + -
112I CYS 5.4 2.3 - - - +
113I GLY* 5.8 2.4 - - - -
72K LYS* 3.1 38.3 + - + -
76K GLU* 4.6 0.3 - - - +
105K ILE* 2.8 24.6 + - - +
106K GLU* 3.3 15.7 - - - +
108K VAL* 1.3 77.3 - - - +
110K TYR* 1.3 60.8 + - - +
112K CYS* 3.1 20.9 + - - +
113K GLY 4.0 1.9 + - - -
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Residues in contact with TYR 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I GLU* 2.7 36.1 + - + -
106K GLU 3.0 15.8 + - - +
107K ASN* 3.8 6.3 - - - +
108K VAL 3.2 0.2 - - - -
109K GLU* 1.3 75.8 - - - +
111K ALA* 1.3 61.8 + - - +
112K CYS 3.3 0.9 + - - -
113K GLY* 3.3 10.7 + - - -
117K LEU* 3.3 41.6 - - + +
161K MET* 3.4 20.6 - - + -
445K ALA* 3.6 21.8 - - + +
446K TYR* 3.3 35.4 - + + +
464K GLY* 3.5 26.5 - - - -
465K PRO* 3.7 18.4 - - - +
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Residues in contact with ALA 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K MET* 4.3 10.3 - - + -
107K ASN 3.3 11.2 + - - +
108K VAL* 3.0 13.0 + - - +
110K TYR* 1.3 76.9 - - - +
112K CYS* 1.3 63.4 + - - +
113K GLY 3.1 0.4 - - - -
114K ALA* 3.3 12.5 + - - +
117K LEU* 5.2 0.2 - - - -
160K PRO 4.1 19.3 - - - +
161K MET* 4.2 14.1 - - + +
164K VAL* 3.4 35.1 - - + +
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Residues in contact with CYS 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I PHE* 4.0 11.7 - - + -
109I GLU* 5.5 1.1 - - - +
112I CYS* 5.8 0.7 - - + -
65K ALA* 3.3 25.1 - - - +
68K MET* 3.5 10.1 - - - -
69K PHE* 3.4 69.3 - - + -
72K LYS* 5.2 0.9 - - - -
108K VAL* 3.1 20.1 + - - -
109K GLU* 3.1 12.9 + - - +
111K ALA* 1.3 79.5 - - - +
113K GLY* 1.3 54.7 + - - +
114K ALA 3.3 1.0 + - - -
115K PRO* 4.2 2.6 - - - +
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Residues in contact with GLY 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I GLU 5.8 3.1 - - - -
110I TYR* 6.5 1.1 - - - -
113I GLY* 5.5 11.3 - - - -
109K GLU 4.0 2.6 + - - -
110K TYR 3.3 12.9 + - - -
111K ALA 3.1 1.0 - - - -
112K CYS* 1.3 76.4 - - - +
114K ALA* 1.3 63.4 + - - -
115K PRO* 3.3 6.5 - - - -
116K GLU* 3.3 16.6 + - - +
117K LEU* 3.3 17.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il