Contacts of the helix formed by residues 99 - 116 (chain K) in PDB entry 3LUE
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 MET 99 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASP* 3.0 43.5 - - + +
341C ILE* 4.3 8.7 - - + -
98K LYS* 1.3 89.0 - - + +
100K ARG* 1.3 67.3 + - - +
101K PHE* 3.3 41.1 - - + -
102K HIS* 3.0 29.7 + - + +
103K LYS* 3.2 11.7 + - - +
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Residues in contact with ARG 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A MET 3.8 0.2 - - - -
48A GLY* 2.4 50.4 - - - +
144C ALA 5.8 2.7 - - - +
145C SER 4.4 2.9 - - - -
146C GLY* 3.8 30.8 + - - -
148C THR* 4.4 0.6 - - - +
98K LYS 3.9 0.2 + - - -
99K MET* 1.3 72.9 - - - +
101K PHE* 1.3 68.5 + - + +
103K LYS* 3.0 15.0 + - - +
104K ILE* 3.0 28.5 + - + +
127K GLU* 3.9 15.0 + - - +
130K VAL* 4.3 15.4 - - + +
131K ASP* 2.6 40.2 + - - -
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Residues in contact with PHE 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLN* 5.6 0.5 - - - +
23C GLY* 5.8 1.6 - - - -
24C ASP 5.3 4.0 - - - -
25C ASP* 4.6 1.6 - - - -
143C TYR* 5.0 6.1 - - + +
144C ALA 4.9 7.6 - - - -
341C ILE* 3.8 17.9 - - + -
344C SER* 5.5 2.5 - - - -
345C ILE* 1.9 75.8 - - + +
348C SER* 5.4 0.4 - - - -
349C LEU* 4.4 4.6 - - - +
99K MET* 3.3 37.2 - - + -
100K ARG* 1.3 80.6 - - + +
102K HIS* 1.3 102.5 + + - +
104K ILE* 3.5 12.7 + - + +
105K ALA* 3.0 23.4 + - - +
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Residues in contact with HIS 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLY* 4.3 24.7 + - - -
24C ASP 6.3 0.2 - - - -
25C ASP* 4.6 3.0 + - - -
348C SER* 5.2 5.6 + - - -
95K ASP* 4.5 17.0 + - + +
96K LYS 3.4 20.0 + - - +
97K GLY* 3.5 30.9 - - - +
99K MET* 3.0 47.4 + - + +
101K PHE* 1.3 99.0 - + - +
103K LYS* 1.3 58.1 + - + +
105K ALA* 3.4 6.6 + - - +
106K ASN* 3.0 34.6 + - - +
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Residues in contact with LYS 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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74K ARG* 3.7 48.8 - - + +
75K ASN* 3.7 32.3 - - + +
98K LYS* 3.6 26.3 + - - +
99K MET 3.2 9.6 + - - +
100K ARG* 3.0 11.1 + - - +
102K HIS* 1.3 75.6 - - + +
104K ILE* 1.3 59.2 + - - +
106K ASN* 3.2 0.9 + - - +
107K VAL* 2.8 35.2 + - - +
130K VAL* 3.8 19.7 + - + -
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Residues in contact with ILE 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 2.9 20.9 - - - -
49A GLN* 1.6 83.5 - - + +
50A LYS* 4.2 1.8 - - + +
349C LEU* 6.3 0.4 - - + -
100K ARG* 3.0 25.9 + - + +
101K PHE* 3.7 11.9 - - + +
102K HIS 3.4 0.2 - - - -
103K LYS* 1.3 74.9 - - - +
105K ALA* 1.3 59.7 + - - +
107K VAL 3.8 0.2 - - - -
108K ASN* 2.9 41.4 + - - +
126K ALA* 3.9 9.6 - - + +
127K GLU* 5.1 2.7 - - - -
130K VAL* 3.7 20.4 - - + -
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Residues in contact with ALA 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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349C LEU* 3.1 34.5 - - + -
95K ASP* 4.2 18.2 - - - +
101K PHE 3.0 12.8 + - - +
102K HIS* 3.6 5.8 - - - +
103K LYS 3.2 0.2 - - - -
104K ILE* 1.3 78.6 - - - +
106K ASN* 1.3 63.2 + - - +
108K ASN* 3.3 7.5 + - - +
109K LYS* 3.1 28.3 + - - +
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Residues in contact with ASN 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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75K ASN 3.7 18.1 + - - +
76K GLY* 4.6 3.4 - - - -
77K LEU* 4.1 14.4 - - + +
80K MET* 3.5 17.1 - - - +
94K PRO* 3.2 9.7 - - - +
95K ASP* 2.7 47.4 + - - +
97K GLY 5.3 1.6 + - - -
102K HIS* 3.0 22.8 + - - +
103K LYS 3.2 0.4 + - - +
105K ALA* 1.3 74.9 - - - +
107K VAL* 1.3 64.4 + - - +
109K LYS* 3.0 31.1 + - - +
110K ALA 3.3 8.0 + - - -
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Residues in contact with VAL 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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73K PHE 4.0 0.2 - - - +
74K ARG 3.8 15.3 - - - +
76K GLY* 3.7 23.1 - - - +
79K LEU* 4.7 4.9 - - + -
103K LYS 2.8 23.8 + - - +
104K ILE 4.0 2.5 - - - +
106K ASN* 1.3 72.1 - - - +
108K ASN* 1.3 57.2 + - - +
110K ALA* 3.3 6.8 + - - +
111K LEU* 2.9 35.1 + - + +
126K ALA* 3.5 30.7 - - + -
129K ILE* 3.7 28.3 - - + -
130K VAL* 4.1 4.3 - - + -
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Residues in contact with ASN 108 (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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49A GLN* 4.1 12.3 + - - +
51A ASP* 4.4 15.8 + - - +
52A SER* 5.4 2.4 - - - +
104K ILE* 2.9 32.6 + - - +
105K ALA* 3.6 8.2 - - - +
107K VAL* 1.3 75.6 - - - +
109K LYS* 1.3 60.4 + - - +
111K LEU* 3.8 13.8 - - - +
112K ASP* 2.9 45.0 + - - +
126K ALA* 3.0 24.6 - - - +
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Residues in contact with LYS 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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350C SER* 4.9 17.6 + - - +
80K MET* 3.8 19.7 - - + -
91K LEU* 4.4 3.3 - - - +
92K PRO* 4.4 28.6 - - + +
93K ARG 3.4 21.1 + - - +
95K ASP* 3.2 24.1 + - - -
105K ALA* 3.1 15.8 + - - +
106K ASN* 3.0 35.8 + - - +
108K ASN* 1.3 77.8 - - - +
110K ALA* 1.3 58.1 + - - +
112K ASP* 3.9 4.5 - - - +
113K PHE* 3.0 28.1 + - - +
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Residues in contact with ALA 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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79K LEU* 3.7 26.2 - - + -
80K MET* 4.1 14.3 - - + +
83K LEU* 3.6 25.1 - - + +
91K LEU* 4.2 6.1 - - - -
106K ASN 3.3 3.1 + - - +
107K VAL* 3.5 7.9 - - - +
108K ASN 3.2 0.2 - - - -
109K LYS* 1.3 77.8 - - - +
111K LEU* 1.3 66.3 + - - +
113K PHE* 3.0 4.3 + - - +
114K ILE* 3.0 27.2 + - + +
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Residues in contact with LEU 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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52A SER* 4.2 2.9 - - - +
79K LEU* 5.4 0.2 - - + -
107K VAL* 2.9 25.5 + - + +
108K ASN* 3.8 16.2 - - - +
110K ALA* 1.3 73.4 - - - +
112K ASP* 1.3 60.0 + - - +
114K ILE* 3.4 8.9 + - + +
115K ALA* 2.9 28.5 + - - +
121K LEU* 3.7 20.7 - - + +
124K ILE* 4.1 22.0 - - + +
125K GLY 3.8 5.2 - - - +
126K ALA* 3.4 37.9 - - - +
129K ILE* 4.7 0.9 - - + -
140K MET* 3.8 30.1 - - + -
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Residues in contact with ASP 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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108K ASN* 2.9 34.7 + - - +
109K LYS* 3.9 4.8 - - - +
111K LEU* 1.3 74.8 - - - +
113K PHE* 1.3 61.9 + - - +
115K ALA* 3.2 7.8 + - - +
116K SER* 2.8 31.8 + - - -
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Residues in contact with PHE 113 (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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83K LEU* 4.1 22.7 - - + -
87K SER* 3.7 22.7 - - - -
89K GLU* 3.8 21.3 - - + -
90K ARG 5.1 2.7 - - - -
91K LEU* 3.6 40.6 - - + -
92K PRO* 5.7 3.4 - - + -
109K LYS 3.0 15.3 + - - +
110K ALA 3.0 8.3 + - - +
112K ASP* 1.3 76.1 - - - +
114K ILE* 1.3 62.7 + - - +
116K SER* 2.5 27.1 + - - -
117K LYS* 3.4 28.7 + - - +
148K PHE* 3.7 23.1 - + - -
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Residues in contact with ILE 114 (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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83K LEU* 4.0 23.1 - - + -
110K ALA* 3.0 22.6 + - + +
111K LEU* 3.5 13.2 - - + +
113K PHE* 1.3 75.7 - - - +
115K ALA* 1.3 61.1 + - - +
117K LYS* 2.9 25.3 + - - +
119K VAL* 3.2 45.3 - - + +
121K LEU* 4.0 10.3 - - + -
140K MET* 4.5 14.4 - - + +
143K THR* 4.4 6.3 - - + +
144K ILE* 3.4 35.2 - - + -
148K PHE* 4.6 6.3 - - + -
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Residues in contact with ALA 115 (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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68A LYS* 5.2 9.4 - - - -
111K LEU 2.9 12.5 + - - +
112K ASP* 3.6 10.1 - - - +
114K ILE* 1.3 76.8 - - - +
116K SER* 1.3 61.9 + - - +
117K LYS 3.0 1.4 + - - -
118K GLY* 3.1 12.5 + - - -
119K VAL 3.2 20.3 + - - +
121K LEU* 3.4 20.8 - - + +
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Residues in contact with SER 116 (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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112K ASP 2.8 14.3 + - - -
113K PHE* 2.5 30.9 + - - -
115K ALA* 1.3 76.4 - - - +
117K LYS* 1.3 62.9 + - - +
118K GLY 3.1 4.7 + - - -
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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
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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