Contacts of the helix formed by residues 110 - 121 (chain B) in PDB entry 3ANX
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 ASP 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B THR* 2.5 28.7 + - - +
31B PRO* 5.0 0.2 - - - +
32B PHE* 3.7 26.3 - - + +
33B GLN* 3.7 14.6 - - - +
108B ASP* 3.5 9.0 + - - +
109B ILE* 1.3 83.4 - - + +
111B GLY* 1.3 57.9 + - - +
112B GLU* 3.2 11.8 + - - +
113B LEU* 2.7 42.4 + - + +
114B VAL* 3.1 19.8 + - - +
138B ILE* 4.7 3.2 + - - +
315B MTA 4.0 8.3 - - - +
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASP* 1.3 71.5 - - - +
112B GLU* 1.3 59.2 + - - +
113B LEU 3.3 0.9 - - - -
114B VAL* 3.6 6.2 + - - +
115B GLU* 2.9 36.0 + - - +
138B ILE* 3.2 38.8 - - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LYS 4.5 1.4 + - - -
30B THR* 3.3 33.9 + - + +
31B PRO* 3.0 22.7 - - + +
35B TYR* 5.1 4.7 - - + +
110B ASP* 3.2 7.2 - - - +
111B GLY* 1.3 75.6 - - - +
113B LEU* 1.3 65.9 + - - +
115B GLU* 2.9 17.3 + - + +
116B VAL* 3.0 17.6 + - + +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B THR* 4.3 3.8 - - + +
33B GLN* 4.6 9.0 - - + +
35B TYR* 4.3 25.6 - - + -
47B LEU* 5.0 9.2 - - + -
49B LEU* 4.5 14.8 - - + -
87B GLY* 4.1 13.5 - - - -
88B GLU* 5.1 1.3 - - + +
110B ASP* 2.7 34.1 + - - +
112B GLU* 1.3 74.5 - - - +
114B VAL* 1.3 69.4 + - - +
115B GLU 2.8 1.1 - - - -
116B VAL* 2.7 29.3 + - + +
117B ALA* 3.0 12.5 + - + +
121B MET* 6.2 2.5 - - - -
315B MTA 3.7 33.4 - - + +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLY* 4.1 18.8 - - - +
106B MET* 5.5 1.1 - - - -
108B ASP* 3.9 19.7 - - + +
110B ASP 3.1 15.8 + - - +
111B GLY* 3.7 12.3 - - - +
112B GLU 3.3 0.2 - - - -
113B LEU* 1.3 76.0 - - - +
115B GLU* 1.3 68.4 + - - +
117B ALA* 3.3 8.3 + - - +
118B LYS* 2.9 38.9 + - + +
129B PHE* 4.1 19.1 - - + -
136B LEU* 4.2 23.1 - - + -
138B ILE* 4.8 1.8 - - + -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLY* 2.9 28.0 + - - +
112B GLU* 2.9 11.0 + - - +
113B LEU 2.7 3.0 + - - -
114B VAL* 1.3 81.1 - - - +
116B VAL* 1.3 51.0 + - - +
118B LYS* 3.1 41.5 + - - +
119B ARG* 2.7 36.2 + - - +
136B LEU* 5.1 1.0 - - - +
138B ILE* 5.2 2.6 - - - +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA* 4.8 3.4 - - + -
35B TYR* 4.0 42.0 - - + +
37B LEU* 4.7 10.5 - - + -
47B LEU* 6.4 2.2 - - + -
112B GLU* 3.0 15.9 + - + +
113B LEU* 2.7 27.8 + - + +
115B GLU* 1.3 69.4 - - - +
117B ALA* 1.3 56.9 + - - +
119B ARG* 2.9 5.0 + - - +
120B HIS* 2.5 65.8 + - + -
121B MET* 4.6 3.8 - - + -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLY 3.7 23.8 - - - +
88B GLU* 3.9 20.4 - - - +
113B LEU* 3.0 11.2 + - + +
114B VAL 3.4 8.1 - - - +
116B VAL* 1.3 75.5 - - - +
118B LYS* 1.3 68.1 + - - +
121B MET* 2.7 42.3 + - + +
125B HIS* 3.2 8.8 - - - -
129B PHE* 4.7 2.5 - - + -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 2.9 21.4 + - + +
115B GLU* 3.3 41.4 + - - +
117B ALA* 1.3 78.0 - - - +
119B ARG* 1.3 63.7 + - - +
121B MET 3.9 1.0 + - - -
122B PRO* 4.3 2.8 - - - +
125B HIS* 3.1 23.3 + - + +
129B PHE* 4.1 32.3 - - + -
130B ASP* 5.7 2.9 - - - -
136B LEU* 3.3 31.5 - - - +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU 2.7 19.3 + - - +
116B VAL* 4.0 2.0 - - - +
118B LYS* 1.3 73.8 - - - +
120B HIS* 1.3 95.4 + - + +
122B PRO* 4.4 4.4 - - - +
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Residues in contact with HIS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 4.0 23.2 + - + +
26B ALA* 4.0 15.8 - - + +
37B LEU* 3.5 18.8 - - + +
45B LYS* 2.6 36.2 + - - +
116B VAL* 2.5 38.4 + - + +
119B ARG* 1.3 120.0 + - + +
121B MET* 1.3 53.7 + - - +
122B PRO* 2.9 8.4 - - - +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.9 26.2 - - + -
47B LEU* 4.0 27.4 - - + -
55B SER* 5.0 0.4 - - - -
88B GLU* 3.9 17.3 - - + -
113B LEU* 6.2 2.9 - - - -
116B VAL* 4.5 3.1 - - - +
117B ALA* 2.7 40.0 + - + +
120B HIS* 1.3 82.4 - - - +
122B PRO* 1.4 63.0 - - - +
123B GLU* 3.2 4.0 - - - -
124B TRP* 3.0 77.5 + - + +
125B HIS* 3.4 7.2 + - - -
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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
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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