Contacts of the helix formed by residues 60 - 78 (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 PRO 60 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K ASN 3.4 7.4 - - - +
59K THR* 1.3 91.1 - - + +
61K PRO* 1.3 73.0 - - + +
62K LEU* 4.3 6.3 - - + +
63K LYS* 2.9 27.4 + - + +
64K ARG* 3.0 11.0 + - - +
125L ASN* 3.4 15.9 - - + +
126L VAL 4.2 8.3 - - - +
127L GLY* 3.9 24.9 - - - +
128L PRO* 3.9 17.3 - - + -
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Residues in contact with PRO 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446I TYR* 5.1 4.5 - - - +
59K THR 3.4 5.1 - - - +
60K PRO* 1.3 81.9 - - + +
62K LEU* 1.3 65.5 + - - +
64K ARG* 3.6 18.8 - - + +
65K ALA* 2.8 26.7 + - - +
114K ALA* 4.7 2.3 - - + +
115K PRO* 3.9 24.8 - - + +
118K LEU* 4.1 29.8 - - + -
164K VAL 5.1 0.9 - - - +
124L ARG* 3.7 17.3 - - - +
125L ASN* 3.3 18.4 - - + +
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Residues in contact with LEU 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I GLU* 4.1 19.3 - - + +
109I GLU* 3.4 26.2 - - + +
444I VAL* 3.6 29.6 - - + -
445I ALA* 6.0 0.7 - - + -
446I TYR* 3.7 24.8 + - + +
60K PRO* 3.2 6.8 + - + +
61K PRO* 1.3 79.6 - - - +
63K LYS* 1.3 63.6 + - - +
65K ALA* 3.2 5.6 + - + +
66K ARG* 3.0 43.3 + - - +
115K PRO* 3.9 9.3 - - + +
126L VAL 4.1 13.2 - - - +
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Residues in contact with LYS 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K TRP* 5.3 1.3 - - + -
59K THR* 3.7 22.3 - - + +
60K PRO* 2.9 21.9 + - + +
62K LEU* 1.3 75.8 - - - +
64K ARG* 1.3 67.8 + - - +
66K ARG* 3.1 29.4 + - + +
67K VAL* 3.6 10.2 + - + +
70K ARG* 5.4 1.9 + - - +
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Residues in contact with ARG 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K TRP* 3.3 64.5 + - + +
57K ARG 3.5 13.7 + - - -
59K THR* 2.9 36.2 + - + +
60K PRO 3.0 17.6 + - - +
61K PRO* 3.6 15.9 - - - +
63K LYS* 1.3 76.5 - - - +
65K ALA* 1.3 61.8 + - - +
67K VAL* 3.3 18.5 - - - +
68K MET* 3.9 3.5 + - - +
118K LEU* 3.7 17.8 - - - +
138K PRO* 4.9 2.8 - - - +
163K ILE* 3.8 1.0 - - - +
164K VAL* 2.6 41.0 + - + +
165K CYS 3.3 15.2 + - - -
166K GLY* 3.2 12.3 - - - +
124L ARG* 4.7 7.3 - - - +
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Residues in contact with ALA 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K PRO 2.8 21.7 + - - +
62K LEU* 3.5 6.3 - - + +
64K ARG* 1.3 71.8 - - - +
66K ARG* 1.3 59.5 + - - +
68K MET* 2.8 22.1 + - - +
69K PHE* 3.0 17.6 + - + -
111K ALA 4.1 0.4 - - - +
112K CYS* 3.3 30.9 - - - +
114K ALA* 4.4 4.0 - - + -
115K PRO* 4.5 3.8 - - + -
164K VAL* 3.6 17.0 - - + +
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Residues in contact with ARG 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LYS* 4.7 7.0 - - - +
76I GLU* 5.7 3.3 + - - -
102I GLN* 4.1 20.9 - - - +
105I ILE* 5.3 0.2 - - - +
106I GLU* 3.3 27.5 + - - +
109I GLU* 2.6 51.4 + - - +
62K LEU* 3.0 34.7 + - - +
63K LYS* 3.1 18.6 + - + +
65K ALA* 1.3 77.5 - - - +
67K VAL* 1.3 61.8 + - - +
69K PHE* 3.3 11.0 + - + +
70K ARG* 3.1 52.7 + - - +
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Residues in contact with VAL 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K TRP* 4.1 17.5 - - + -
63K LYS* 3.9 9.0 - - + +
64K ARG 3.3 14.4 - - - +
66K ARG* 1.3 77.2 - - - +
68K MET* 1.3 56.1 + - - +
70K ARG* 3.3 15.2 + - - +
71K PHE* 2.8 31.2 + - - +
163K ILE* 6.0 0.4 - - + -
188K LEU* 4.4 10.3 - - + -
191K ALA* 3.5 18.8 - - + +
192K GLY 4.0 17.7 - - - +
193K LEU* 4.1 29.4 - - + +
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Residues in contact with MET 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K ARG 4.2 3.6 - - - +
65K ALA 2.8 10.4 + - - +
67K VAL* 1.3 82.0 - - - +
69K PHE* 1.3 61.3 + - - +
71K PHE* 3.5 33.9 - - + -
72K LYS* 3.0 24.1 + - - +
108K VAL* 3.3 22.7 - - + +
111K ALA* 4.3 7.4 - - + -
112K CYS* 3.5 16.6 - - - +
159K PHE* 5.8 0.4 - - + -
160K PRO* 3.6 40.6 - - + +
163K ILE* 5.2 11.7 - - - -
164K VAL* 4.1 23.6 - - + -
188K LEU* 4.7 7.0 - - + -
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Residues in contact with PHE 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I PHE* 3.3 38.8 - + - -
72I LYS* 3.4 35.9 - - + +
109I GLU* 3.9 42.2 - - + -
112I CYS* 4.0 11.7 - - + -
65K ALA* 3.0 25.9 + - + -
66K ARG* 3.3 14.3 + - + +
68K MET* 1.3 78.4 - - - +
70K ARG* 1.3 62.8 + - + +
72K LYS* 3.6 14.6 + - - +
73K GLU* 3.7 13.4 + - - +
112K CYS* 3.4 34.9 - - + -
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Residues in contact with ARG 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LYS* 6.0 1.8 - - - +
76I GLU* 6.0 0.2 + - - -
63K LYS* 5.4 1.8 + - - +
66K ARG* 3.1 50.3 + - - +
67K VAL* 3.7 15.6 - - - +
69K PHE* 1.3 75.8 - - + +
71K PHE* 1.3 65.7 + - - +
73K GLU* 3.3 19.1 + - - +
74K LEU* 3.3 25.5 + - + +
190K GLU 5.5 0.9 - - - -
191K ALA* 3.0 38.7 + - + +
192K GLY* 4.6 5.1 + - - -
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Residues in contact with PHE 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K VAL 2.8 17.7 + - - +
68K MET* 3.5 32.1 - - + +
70K ARG* 1.3 75.3 - - - +
72K LYS* 1.3 64.6 + - - +
74K LEU* 3.3 3.8 + - + +
75K LEU* 3.1 53.6 + - + +
108K VAL* 3.9 8.3 - - + -
156K LEU* 3.5 28.3 - - + -
159K PHE* 4.2 11.9 - + - -
184K ILE* 3.3 27.6 - - + -
187K LEU* 4.1 11.2 - - + -
188K LEU* 3.6 34.5 - - + -
191K ALA* 3.7 5.3 - - + +
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Residues in contact with LYS 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ARG* 5.0 9.3 + - - +
69I PHE* 3.5 47.9 - - + +
70I ARG* 6.2 1.6 - - - +
73I GLU* 5.8 2.0 + - - -
68K MET 3.0 17.0 + - - +
69K PHE* 3.6 7.0 - - - +
71K PHE* 1.3 76.5 - - - +
73K GLU* 1.3 63.6 + - + +
75K LEU* 3.5 7.5 + - - +
76K GLU* 2.6 54.6 + - - +
105K ILE* 3.8 11.1 - - + +
108K VAL* 4.0 12.7 - - + +
109K GLU* 3.1 36.2 + - + -
112K CYS* 5.2 0.7 - - - -
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Residues in contact with GLU 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I GLU* 3.1 45.6 - - - +
69K PHE 3.7 12.9 + - - +
70K ARG* 3.3 19.5 + - - +
71K PHE 3.2 0.4 - - - -
72K LYS* 1.3 80.1 - - + +
74K LEU* 1.3 60.9 + - + +
76K GLU* 3.2 12.7 + - - +
77K GLN* 2.9 49.9 + - - +
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Residues in contact with LEU 74 (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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70K ARG* 3.3 16.1 + - + +
71K PHE* 3.3 6.7 + - - +
73K GLU* 1.3 77.1 - - + +
75K LEU* 1.3 58.9 + - - +
77K GLN* 4.3 14.4 - - - +
78K HIS* 2.9 51.2 + - + +
187K LEU* 3.4 44.0 - - + +
190K GLU* 3.9 30.5 - - + +
191K ALA* 3.7 23.6 - - + +
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Residues in contact with LEU 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K PHE* 3.1 62.2 + - + +
72K LYS* 3.7 6.3 - - - +
74K LEU* 1.3 76.2 - - - +
76K GLU* 1.3 61.4 + - - +
78K HIS 3.7 1.4 - - - -
79K ALA* 3.3 22.9 + - - +
82K ILE* 3.8 11.2 - - + +
101K LEU* 3.8 8.2 - - + +
105K ILE* 3.9 24.2 - - + -
108K VAL* 3.8 18.4 - - + -
156K LEU* 4.3 11.7 - - + -
184K ILE* 4.0 19.3 - - + -
187K LEU* 3.8 14.4 - - + -
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Residues in contact with GLU 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ARG* 5.7 1.4 - - - -
73I GLU* 5.2 2.9 - - - +
72K LYS* 2.6 52.4 + - - +
73K GLU* 3.2 16.3 + - - +
75K LEU* 1.3 75.8 - - - +
77K GLN* 1.3 63.4 + - + +
79K ALA* 3.3 19.3 - - - +
102K GLN* 5.4 4.1 + - - +
105K ILE* 3.9 22.5 - - + +
109K GLU* 4.6 0.5 - - - +
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Residues in contact with GLN 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K GLU* 2.9 40.9 + - - +
74K LEU* 3.8 18.1 - - - +
76K GLU* 1.3 77.8 - - + +
78K HIS* 1.3 68.5 + - + +
79K ALA 3.3 2.0 + - - -
80K ASP 5.1 0.2 + - - -
81K GLU* 4.1 6.9 - - - +
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Residues in contact with HIS 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74K LEU* 2.9 40.5 + - + +
75K LEU 3.7 3.1 - - - -
77K GLN* 1.3 84.2 + - + +
79K ALA* 1.3 62.3 + - - -
80K ASP 3.3 2.9 - - - -
81K GLU* 3.3 23.5 + - - +
82K ILE* 3.2 25.5 + - + +
183K TYR* 3.2 35.2 + - + +
187K LEU* 3.4 25.2 - - + +
190K GLU* 4.8 6.2 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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