Contacts of the strand formed by residues 78 - 84 (chain C) in PDB entry 6H25
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 TYR 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C ALA 4.4 11.9 - - - -
69C PRO* 5.0 4.3 - - + -
70C SER* 3.3 38.2 + - - -
73C ALA* 5.8 4.9 - - + -
76C LYS* 4.3 5.4 + - + -
77C GLY* 1.3 77.2 - - - -
79C VAL* 1.3 61.6 + - - +
80C VAL* 4.9 3.4 - - + -
121C LYS* 5.9 0.2 - - - +
124C LEU* 4.0 6.4 - - - +
132C VAL* 5.1 4.3 - - + +
133C TRP 3.5 7.1 + - - +
134C VAL* 3.6 23.4 - - + +
135C LEU 3.3 18.4 + - - -
10F GLY* 4.2 7.0 + - - -
11F PRO* 3.6 47.8 - - + -
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLY 4.7 0.2 - - - +
78C TYR* 1.3 76.3 - - - +
80C VAL* 1.3 66.9 + - - +
81C PRO* 3.6 7.1 - - - +
113C ILE* 4.0 37.0 - - + -
119C ILE* 5.0 11.2 - - + -
121C LYS* 4.1 24.2 - - + +
124C LEU* 5.3 4.0 - - + -
135C LEU* 3.4 27.6 - - + +
137C CYS* 4.4 14.8 - - - -
160C LEU* 5.8 4.7 - - + -
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR* 4.9 4.0 - - + -
79C VAL* 1.3 81.3 - - - +
81C PRO* 1.3 71.8 - - + +
82C ASN* 5.3 3.8 - - + +
134C VAL* 5.0 0.9 - - + +
135C LEU 2.9 9.1 + - - -
136C TYR* 3.6 30.6 - - + -
137C CYS* 2.9 26.1 + - - +
138C ASP* 5.3 0.9 - - - +
8F ILE* 3.6 28.3 - - + +
9F ARG 4.5 2.9 - - - +
10F GLY* 3.8 27.4 - - - +
11F PRO* 4.2 4.5 - - + -
110F ARG* 6.2 1.1 - - - +
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Residues in contact with PRO 81 (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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79C VAL 3.6 9.6 - - - +
80C VAL* 1.3 95.5 - - + +
82C ASN* 1.3 62.8 + - - +
83C VAL 4.3 0.2 - - - -
106C SER* 4.5 4.8 - - - +
109C ILE* 3.7 24.5 - - + -
110C ALA* 3.8 37.2 - - + +
113C ILE* 4.0 17.7 - - + -
137C CYS* 3.2 14.4 - - + +
139C LEU* 5.2 1.3 - - + -
8F ILE* 4.1 21.2 - - + +
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Residues in contact with ASN 82 (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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80C VAL* 5.3 4.3 - - + +
81C PRO* 1.3 77.9 - - - +
83C VAL* 1.3 70.6 + - - +
84C ASP* 3.7 9.8 + - - +
106C SER* 3.7 10.7 + - - -
137C CYS 2.9 8.1 + - - -
138C ASP* 3.4 19.1 + - - +
139C LEU* 2.9 24.5 + - - +
7F ARG* 3.6 40.5 + - - +
8F ILE* 5.4 3.5 + - - +
110F ARG* 5.3 2.1 - - - +
113F PRO* 4.1 18.4 - - - +
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Residues in contact with VAL 83 (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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82C ASN* 1.3 76.6 + - - +
84C ASP* 1.3 64.1 + - - +
85C LEU* 4.6 13.0 - - + -
98C PRO* 5.8 0.2 - - - +
102C ALA* 3.6 16.1 - - - +
105C ALA* 4.1 16.6 - - + +
106C SER* 3.0 27.1 + - - +
109C ILE* 3.8 30.1 - - + -
139C LEU* 3.5 33.2 - - + +
141C CYS* 5.8 1.3 - - + +
148C ILE* 5.2 1.1 - - + -
152C CYS* 3.9 20.4 - - - -
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Residues in contact with ASP 84 (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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82C ASN* 3.7 12.8 + - - +
83C VAL* 1.3 74.2 - - - +
85C LEU* 1.3 84.9 + - - +
86C PRO* 3.5 14.5 - - + +
98C PRO* 4.4 16.5 - - - +
102C ALA* 4.7 0.9 - - - -
139C LEU 2.9 18.3 + - - +
140C ILE* 3.9 12.3 - - + +
141C CYS 3.6 6.1 + - - -
7F ARG* 5.5 8.8 + - - -
101F ARG* 4.5 17.6 + - - -
113F PRO* 5.1 11.0 - - - +
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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