Contacts of the helix formed by residues 117 - 125 (chain B) in PDB entry 6V99
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 ASN 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B TYR* 2.9 30.7 + - + +
95B LEU* 3.7 33.0 - - + +
100B ARG* 3.8 15.6 + - - -
107B TYR* 3.0 22.9 + - - -
113B ALA 2.9 15.4 + - - -
114B VAL 3.0 7.1 + - - +
116B GLN* 1.3 78.8 - - - +
118B ILE* 1.3 64.8 + - - +
119B ASP* 3.1 8.5 - - - -
120B ILE* 3.0 17.0 + - + +
121B ILE* 3.2 14.6 + - + +
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Residues in contact with ILE 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 3.9 7.4 - - - +
115B TYR* 3.1 46.5 + - + +
116B GLN 3.5 0.8 - - - -
117B ASN* 1.3 76.8 - - - +
119B ASP* 1.3 59.4 + - - +
121B ILE* 3.0 6.9 + - + -
122B GLU* 2.9 60.0 + - + +
217B MET* 3.7 24.9 - - + +
220B LEU* 4.3 11.7 - - + -
221B ARG* 3.7 23.1 - - + +
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Residues in contact with ASP 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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100B ARG* 2.8 33.6 + - - -
101B VAL* 4.1 12.8 - - + +
116B GLN 3.6 10.9 - - - +
117B ASN* 3.6 10.9 - - - -
118B ILE* 1.3 76.7 - - - +
120B ILE* 1.3 67.1 + - - +
122B GLU* 5.2 1.6 - - - -
123B PRO* 3.1 24.6 - - - +
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Residues in contact with ILE 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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14B MET* 5.2 4.3 - - + -
93B ASP* 3.9 29.8 - - + +
95B LEU* 4.0 26.9 - - + -
100B ARG* 4.7 11.0 - - - +
117B ASN* 3.0 18.0 + - + +
119B ASP* 1.3 97.9 - - - +
121B ILE* 1.3 65.6 + - + +
123B PRO* 3.6 8.4 - - - +
124B TYR* 3.4 23.7 + - + +
71C HIS* 5.2 11.4 - - + +
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Residues in contact with ILE 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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14B MET* 3.9 27.1 - - + -
16B TYR* 4.1 13.5 - - + -
114B VAL* 3.8 29.8 - - + +
117B ASN 3.5 19.1 - - - +
118B ILE* 3.0 8.2 + - - +
120B ILE* 1.3 78.4 - - + +
122B GLU* 1.3 66.4 + - - +
124B TYR* 2.9 22.4 + - - +
125B ALA 3.3 3.6 + - - -
126B PRO* 3.5 13.3 - - + +
129B MET* 3.8 27.8 - - + -
213B THR* 4.5 4.7 - - + -
217B MET* 4.3 17.9 - - + -
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Residues in contact with GLU 122 (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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118B ILE* 2.9 33.2 + - + +
119B ASP* 5.2 1.5 - - - -
121B ILE* 1.3 76.7 - - + +
123B PRO* 1.3 64.3 - - + +
125B ALA* 2.8 26.6 + - - +
126B PRO* 5.2 0.7 - - - -
213B THR* 6.1 1.8 - - + -
214B LYS* 3.1 26.6 + - - +
217B MET* 3.7 14.1 - - + +
221B ARG* 3.3 26.9 + - - -
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Residues in contact with PRO 123 (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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119B ASP* 3.1 28.0 - - - +
120B ILE 3.6 8.3 - - - +
122B GLU* 1.3 93.5 - - + +
124B TYR* 1.3 64.3 + - + +
125B ALA* 3.4 3.5 + - - +
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Residues in contact with TYR 124 (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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14B MET* 4.3 18.2 - - + -
61B ARG* 3.3 48.7 + - - +
91B SER* 3.4 24.0 - - - -
93B ASP* 2.8 33.6 + - - -
120B ILE* 3.4 26.5 - - + +
121B ILE 2.9 10.0 + - - +
123B PRO* 1.3 81.6 - - + +
125B ALA* 1.3 67.5 + - - +
126B PRO* 3.2 9.5 - - + +
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Residues in contact with ALA 125 (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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122B GLU* 2.8 17.8 + - - +
123B PRO 4.3 3.4 - - - +
124B TYR* 1.3 79.2 - - - +
126B PRO* 1.3 72.5 - - - +
127B GLU* 3.6 1.4 + - - -
213B THR* 5.9 0.7 - - - -
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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
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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