Contacts of the helix formed by residues 110 - 124 (chain K) in PDB entry 6AVO
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 110 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B THR* 5.7 1.8 - - - -
72B ARG* 4.3 19.1 - - - +
101K TRP* 3.9 18.4 - - + +
107K TYR* 3.9 11.2 - - + +
108K GLU 3.2 8.7 - - - +
109K ILE* 1.3 91.7 - - + +
111K VAL* 1.3 66.3 - - - +
112K ASP* 2.9 22.0 - - - +
113K MET* 3.1 9.3 + - + -
114K LEU* 3.0 18.9 + - - +
144K ASP* 4.2 20.9 - - + +
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Residues in contact with VAL 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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76K ILE* 4.3 19.5 - - + -
109K ILE 4.6 0.4 - - - -
110K PRO* 1.3 72.4 - - - +
112K ASP* 1.3 58.6 + - - +
114K LEU* 4.3 5.6 - - - -
115K CYS* 2.9 29.1 + - - +
140K LEU* 3.9 29.2 - - + -
141K ILE 4.2 1.3 - - - -
142K GLY* 3.4 39.9 - - - +
144K ASP* 5.8 3.5 - - + +
150K GLN* 4.2 19.2 - - + +
152K TYR* 4.0 17.5 - - + +
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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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70B THR 4.3 7.7 - - - +
72B ARG* 3.3 24.5 + - - -
110K PRO* 2.9 21.7 - - - +
111K VAL* 1.3 73.9 - - - +
113K MET* 1.3 82.8 + - - +
115K CYS* 4.3 0.5 - - - +
116K LYS* 2.9 30.3 + - - +
147K GLN* 5.4 2.3 - - - +
150K GLN* 5.1 3.9 - - - +
152K TYR* 3.2 35.0 + - + +
160K TYR* 4.7 4.8 - - + -
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Residues in contact with MET 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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69B SER* 3.9 35.7 - - - +
70B THR* 4.1 17.5 - - + +
101K TRP* 3.9 41.8 - - + -
109K ILE* 4.1 7.9 - - + +
110K PRO* 3.1 10.4 + - + +
112K ASP* 1.3 93.2 + - - +
114K LEU* 1.3 61.6 + - - +
116K LYS* 3.7 27.8 - - + +
117K ARG* 2.9 30.6 + - + +
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Residues in contact with LEU 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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72K ILE* 3.8 25.8 - - + -
76K ILE* 3.9 20.4 - - + -
94K ALA* 3.9 12.6 - - + +
97K GLU* 3.9 28.7 - - + -
98K ALA 4.5 2.2 - - - +
109K ILE* 3.8 19.7 - - + +
110K PRO 3.0 15.0 + - - +
111K VAL* 3.3 6.3 + - - +
113K MET* 1.3 77.4 - - - +
115K CYS* 1.3 59.7 + - - +
117K ARG* 3.0 4.8 + - + +
118K ILE* 2.9 40.9 + - + +
140K LEU* 3.7 22.7 - - + -
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Residues in contact with CYS 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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111K VAL 2.9 17.0 + - - +
114K LEU* 1.3 74.5 - - - +
116K LYS* 1.3 61.6 + - - +
118K ILE* 4.0 4.4 - - - +
119K ALA* 2.9 23.4 + - - +
138K MET 4.9 0.2 - - - -
140K LEU* 3.5 20.9 - - + -
152K TYR* 3.8 31.2 - - + -
154K CYS* 3.4 41.1 - - - -
160K TYR* 3.9 10.8 - - + -
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Residues in contact with LYS 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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69B SER* 4.3 15.5 + - - +
112K ASP 2.9 22.1 + - - +
113K MET* 3.7 26.7 - - + +
115K CYS* 1.3 77.6 - - - +
117K ARG* 1.3 63.8 + - - +
119K ALA* 3.3 3.8 + - - +
120K ASP* 2.9 35.3 + - - +
160K TYR* 3.4 36.4 - - + +
65b GLU* 6.4 0.2 - - - -
83b ARG* 4.5 15.7 + - - +
86b VAL* 6.0 2.0 - - - +
87b HIS* 6.0 6.5 + - - +
90b ARG* 4.1 21.0 - - - +
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Residues in contact with ARG 117 (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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93K ARG* 4.3 15.8 - - - +
97K GLU* 3.3 42.5 + - + +
101K TRP* 6.5 1.1 - - + -
109K ILE* 5.5 2.9 - - + -
113K MET* 2.9 21.8 + - + +
114K LEU* 3.4 6.1 - - - +
116K LYS* 1.3 75.4 - - - +
118K ILE* 1.3 63.3 + - - +
120K ASP* 2.9 34.5 + - - +
121K ILE* 3.0 21.7 + - + +
87b HIS* 6.2 0.4 + - - -
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Residues in contact with ILE 118 (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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90K GLN* 4.8 19.3 - - + +
93K ARG* 4.4 10.5 - - + -
94K ALA* 3.8 29.6 - - + +
97K GLU* 3.9 19.3 - - + -
114K LEU* 2.9 23.1 + - + +
115K CYS* 4.0 3.4 - - - +
117K ARG* 1.3 73.6 - - - +
119K ALA* 1.3 57.8 + - - +
121K ILE* 2.8 24.7 + - + +
122K SER* 2.9 15.0 + - - +
138K MET* 3.3 36.1 - - + -
154K CYS* 4.2 7.4 - - - -
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Residues in contact with ALA 119 (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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115K CYS 2.9 19.4 + - - +
116K LYS 3.5 4.0 - - - +
118K ILE* 1.3 75.1 - - - +
120K ASP* 1.3 58.1 + - - +
122K SER* 3.1 5.4 + - - +
123K GLN* 2.9 30.3 + - - +
154K CYS* 4.4 8.2 - - + +
158K GLY* 3.0 33.5 - - - +
159K TYR 4.2 3.6 - - - +
160K TYR* 3.8 12.8 - - + -
83b ARG* 3.6 8.3 - - - +
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Residues in contact with ASP 120 (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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116K LYS* 2.9 33.5 + - - +
117K ARG* 2.9 28.9 + - - +
119K ALA* 1.3 75.8 - - - +
121K ILE* 1.3 61.9 + - + +
123K GLN* 3.8 7.6 + - - +
124K VAL* 3.3 26.7 + - - +
80b PRO 5.3 0.7 - - - +
83b ARG* 3.7 31.3 + - - +
84b VAL* 5.1 5.6 + - + +
87b HIS* 5.9 4.5 - - - +
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Residues in contact with ILE 121 (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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93K ARG* 3.1 60.8 - - + +
97K GLU* 3.8 10.3 - - - +
117K ARG* 3.0 33.0 + - + +
118K ILE* 2.8 15.5 + - + +
120K ASP* 1.3 79.9 - - + +
122K SER* 1.3 61.1 + - - +
124K VAL* 4.2 8.8 + - + +
125K TYR* 4.0 32.7 - - + +
134K LEU* 6.3 1.6 - - + -
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Residues in contact with SER 122 (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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90K GLN* 3.5 23.6 + - - -
118K ILE* 2.9 13.5 + - - +
119K ALA* 3.1 6.7 + - - -
121K ILE* 1.3 78.2 - - - +
123K GLN* 1.3 65.2 + - - +
124K VAL 3.2 1.3 - - - -
125K TYR* 3.1 14.2 + - - +
126K THR* 3.0 23.2 + - - +
133K PRO* 5.4 0.4 - - - +
134K LEU* 5.0 6.8 - - - +
154K CYS* 6.0 1.2 - - - -
155K ASP 4.1 19.5 + - - -
156K PRO* 4.3 10.0 - - - +
158K GLY* 4.6 2.5 - - - -
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Residues in contact with GLN 123 (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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119K ALA 2.9 16.3 + - - +
120K ASP* 4.0 9.2 - - - +
122K SER* 1.3 77.8 - - - +
124K VAL* 1.3 68.3 + - - +
126K THR* 2.7 33.4 + - - +
127K GLN* 2.8 37.1 + - - +
158K GLY* 4.6 3.9 - - - -
80b PRO* 3.7 33.0 - - + +
81b ASP* 2.7 26.6 + - - +
83b ARG* 5.2 0.4 - - - +
84b VAL* 3.0 27.0 - - + +
127b ARG* 4.3 0.6 - - - +
129b PHE* 5.1 0.4 - - - -
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Residues in contact with VAL 124 (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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120K ASP 3.3 19.0 + - - +
121K ILE* 4.2 10.8 - - + +
122K SER 3.2 0.4 - - - -
123K GLN* 1.3 84.5 - - - +
125K TYR* 1.3 65.5 + - + +
127K GLN* 4.5 3.6 - - - +
128K ASN* 3.0 53.2 + - - +
131K MET* 5.7 2.0 - - + -
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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
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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