Contacts of the strand formed by residues 116 - 123 (chain C) in PDB entry 1HWG
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 GLY 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C THR* 3.0 2.5 - - - -
113C SER 2.6 38.4 + - - +
114C ASN 2.7 14.1 + - - -
115C GLY* 1.3 73.7 - - - +
117C THR* 1.3 62.5 + - - -
118C VAL* 3.9 2.3 - - - +
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS* 3.4 39.2 + - + +
111C LEU 3.4 6.3 - - - +
112C THR* 3.6 4.2 + - - -
115C GLY 3.8 1.4 + - - -
116C GLY* 1.3 72.6 - - - -
118C VAL* 1.3 63.1 + - - +
119C ASP 3.6 22.9 - - - +
120C GLU* 4.7 7.9 - - + +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLU* 4.5 21.1 - - + +
33C PRO* 3.1 30.7 - - + +
34C LYS* 5.2 2.4 - - - +
64C ILE* 5.7 0.2 - - + -
111C LEU* 2.8 25.9 + - + +
113C SER* 3.3 35.7 - - - +
116C GLY 3.9 4.0 - - - +
117C THR* 1.3 77.4 - - - +
119C ASP* 1.3 63.1 + - - +
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Residues in contact with ASP 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS* 3.9 15.1 - - - +
35C PHE* 2.9 43.6 + - + +
110C LYS* 3.2 3.6 - - - -
111C LEU* 2.7 43.2 + - + -
117C THR* 3.6 7.0 - - - +
118C VAL* 1.3 84.5 - - - +
120C GLU* 1.3 72.0 + - - +
121C LYS* 6.1 0.2 - - - -
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 4.8 1.1 - - - -
80C TRP* 4.1 21.6 - - + -
108C CYS* 6.1 0.2 - - - -
109C ILE 3.3 14.1 - - - +
110C LYS* 4.4 10.2 - - + +
117C THR* 4.7 7.1 - - + +
119C ASP* 1.3 87.3 + - - +
121C LYS* 1.3 71.7 + - - +
122C CYS* 5.3 9.3 - - - -
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 3.7 32.1 - - + +
36C THR 5.1 1.6 + - - -
37C LYS* 4.2 22.0 - - - +
38C CYS* 4.2 13.2 - - - +
108C CYS* 3.2 1.9 - - - +
109C ILE* 2.7 60.3 + - + +
119C ASP* 5.8 0.4 - - - +
120C GLU* 1.3 78.1 - - - +
122C CYS* 1.3 64.1 + - - +
123C PHE* 4.1 13.3 - - + -
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Residues in contact with CYS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A PHE* 4.0 11.4 - - + -
2A PRO* 3.6 22.0 - - + +
107C TYR 3.1 6.3 - - - +
108C CYS* 2.3 44.6 - - - -
120C GLU* 5.3 8.7 - - - -
121C LYS* 1.3 77.3 - - - +
123C PHE* 1.3 68.0 + - - +
127C GLU* 4.8 1.6 - - - +
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Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 3.8 15.5 - - - +
38C CYS* 3.8 23.6 - - - -
46C PHE* 3.6 32.3 - + - -
48C CYS* 4.6 0.7 - - - -
106C PRO* 3.6 1.1 - - - +
107C TYR* 2.8 46.6 + + + +
109C ILE* 4.2 21.5 - - + -
121C LYS* 4.1 18.2 - - + -
122C CYS* 1.3 80.7 - - - +
124C SER* 1.3 76.0 + - - +
125C VAL 4.7 1.3 - - - -
127C GLU* 3.9 11.7 - - - +
128C ILE* 3.4 35.4 - - + -
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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