Contacts of the strand formed by residues 94 - 103 (chain C) in PDB entry 3WHD
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 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C CYS* 3.7 1.0 - - - -
89C ARG 3.9 0.2 - - - +
90C ALA* 3.5 4.0 - - - +
91C PHE 3.0 27.2 + - - +
92C GLN* 3.0 18.0 + - - +
93C SER* 1.3 84.1 + - - +
95C CYS* 1.3 68.1 + - - +
96C TYR* 3.7 24.9 + - + +
127C GLU* 4.9 0.8 + - - -
208C LYS* 3.8 25.0 - - + +
209C ILE 3.7 6.5 - - - +
210C PRO* 3.5 19.8 - - - +
211C GLY 3.9 0.4 - - - +
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Residues in contact with CYS 95 (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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84C CYS* 2.0 55.6 - - + -
85C PRO* 4.1 4.0 - - + -
88C TRP* 3.5 11.4 - - + -
89C ARG 3.3 4.9 - - - -
94C ASN* 1.3 75.5 - - - +
96C TYR* 1.3 64.8 + - - +
208C LYS* 3.3 5.4 - - - +
209C ILE* 2.8 46.5 + - + +
210C PRO 4.3 1.6 - - - -
211C GLY* 3.5 23.1 - - - -
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Residues in contact with TYR 96 (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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88C TRP* 3.3 6.3 - - - +
89C ARG* 2.7 54.1 + - + +
91C PHE* 3.9 25.1 + + + -
94C ASN* 3.7 27.3 + - + +
95C CYS* 1.3 75.6 - - - +
97C PHE* 1.3 63.2 + - - +
98C PRO* 4.1 2.5 - - - -
120C MET* 3.5 29.6 - - + -
127C GLU* 2.4 40.5 + - + +
130C PHE* 4.0 13.5 - + - -
131C ILE* 3.6 20.9 - - + -
206C ILE* 4.4 1.1 - - + -
207C CYS 3.3 6.1 - - - +
208C LYS* 3.5 32.2 - - + -
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Residues in contact with PHE 97 (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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87C ASP* 4.0 35.0 - - + -
88C TRP* 3.4 53.6 - + + -
89C ARG* 6.2 0.2 - - + -
96C TYR* 1.3 76.5 - - - +
98C PRO* 1.3 74.8 - - + +
99C LEU* 3.6 46.3 + - + +
115C MET* 4.2 14.6 - - + -
205C ARG 4.0 0.2 - - - +
206C ILE* 3.6 2.1 - - - +
207C CYS* 2.9 30.3 + - + +
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Residues in contact with PRO 98 (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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89C ARG* 4.5 15.3 - - + +
96C TYR 4.1 3.8 - - - +
97C PHE* 1.3 94.6 - - + +
99C LEU* 1.3 65.8 - - - +
100C THR* 5.3 3.1 - - + +
131C ILE* 4.8 6.7 - - + -
134C PHE* 4.1 28.9 - - + +
135C LEU* 3.9 23.8 - - + -
141C TYR* 4.1 9.0 - - + +
205C ARG 3.3 7.6 - - - +
206C ILE* 4.1 7.2 - - + -
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Residues in contact with LEU 99 (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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97C PHE* 3.7 49.6 - - + +
98C PRO* 1.3 79.9 - - - +
100C THR* 1.3 64.1 + - - +
101C ASP* 3.7 3.8 + - - +
111C ASN* 3.6 23.8 - - - +
115C MET* 4.1 8.5 - - + -
141C TYR* 4.1 1.6 - - - -
204C SER* 3.2 3.8 - - - -
205C ARG* 2.7 64.3 + - + +
207C CYS* 4.1 4.7 - - - -
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Residues in contact with THR 100 (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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98C PRO* 5.3 2.5 - - + +
99C LEU* 1.3 76.8 - - - +
101C ASP* 1.3 67.4 + - - +
102C ASN* 3.6 3.3 + - - +
136C ASP* 5.5 2.0 - - + -
139C LEU* 4.1 17.9 - - + +
141C TYR* 4.0 20.9 - - + +
204C SER* 2.8 20.7 + - - -
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Residues in contact with ASP 101 (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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99C LEU* 4.2 2.9 - - - +
100C THR* 1.3 81.3 + - - +
102C ASN* 1.3 62.9 + - - +
103C LYS* 3.6 19.1 + - - +
203C ALA 3.6 4.7 - - - +
204C SER* 4.0 1.0 - - - -
205C ARG* 2.9 52.9 + - - -
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Residues in contact with ASN 102 (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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100C THR 3.6 2.3 + - - +
101C ASP* 1.3 75.0 - - - +
103C LYS* 1.3 66.3 + - - +
139C LEU* 6.1 0.7 - - - +
202C GLU* 4.1 32.5 + - + +
203C ALA* 3.1 29.7 - - - -
204C SER* 3.6 5.5 + - - -
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Residues in contact with LYS 103 (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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101C ASP* 3.6 11.9 + - - +
102C ASN* 1.3 79.8 - - - +
104C THR* 1.3 67.2 + - - +
107C GLU* 3.7 37.0 + - + +
108C SER* 3.4 14.7 + - - +
110C ARG* 5.8 1.4 - - - +
111C ASN* 4.0 16.4 - - - +
142C PHE* 3.5 2.9 - - - -
202C GLU* 3.8 11.2 - - - -
203C ALA 3.0 28.7 + - - +
205C ARG* 3.6 37.2 - - - +
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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