Contacts of the strand formed by residues 72 - 79 (chain C) in PDB entry 1J7H
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 ILE 72 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU* 6.5 0.4 - - + -
58C VAL* 5.8 2.9 - - + -
62C ILE* 4.6 15.0 - - + -
68C THR 3.7 2.2 + - - +
69C ALA* 2.8 47.7 + - + +
70C ALA 4.1 3.3 - - - +
71C ASP* 1.3 76.9 - - - +
73C VAL* 1.3 57.7 + - - +
74C LYS 3.1 7.0 - - - +
75C THR* 3.0 30.7 - - + +
95C PHE* 6.0 0.4 - - + -
96C PHE* 4.1 13.7 - - + -
103C ASN* 4.1 6.2 + - - -
105C PRO* 3.0 32.1 - - + +
125C ALA* 3.8 9.2 - - + -
126C ILE 3.0 21.1 - - - +
127C ALA* 3.8 9.6 - - + +
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.2 39.2 - - + +
22A VAL* 3.3 13.7 - - - +
24A LEU* 4.4 0.4 - - + -
29A LEU* 5.8 3.8 - - + -
27C LEU* 4.5 3.6 - - + -
71C ASP 3.0 1.3 + - - +
72C ILE* 1.3 73.2 - - - +
74C LYS* 1.3 75.6 + - + +
103C ASN* 5.2 0.2 - - - +
105C PRO* 3.1 5.4 - - - +
106C ALA 2.8 17.5 + - - -
126C ILE* 2.8 37.9 + - + +
128C VAL* 3.0 47.8 - - + +
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Residues in contact with LYS 74 (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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22A VAL* 5.1 2.7 - - + -
29A LEU* 5.0 21.3 - - + +
30A THR 5.0 10.8 - - - +
31A SER* 5.5 0.4 - - - +
124A GLU* 5.6 5.8 - - - -
126A ILE* 5.7 7.7 - - - +
72C ILE* 3.1 2.8 - - - +
73C VAL* 1.3 88.9 - - + +
75C THR* 1.3 80.0 + - - +
76C THR* 3.8 12.9 + - - -
106C ALA* 3.2 31.0 - - + +
107C ARG 4.8 2.5 - - - -
108C SER* 4.3 20.5 - - - -
125C ALA* 3.0 1.7 - - - +
126C ILE* 2.7 40.7 + - + +
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Residues in contact with THR 75 (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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72C ILE* 3.0 20.6 - - + +
74C LYS* 1.3 78.9 + - - +
76C THR* 1.3 70.1 + - - +
77C VAL* 4.0 18.6 - - + -
92C TYR* 3.1 30.7 + - + +
105C PRO* 3.7 5.0 - - - +
106C ALA 2.6 19.7 + - - +
107C ARG* 3.2 6.9 - - - +
108C SER* 2.9 23.4 + - - -
123C ILE* 4.8 6.1 - - + -
125C ALA* 3.2 16.2 - - + +
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Residues in contact with THR 76 (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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78A PHE* 6.2 0.2 - - + -
74C LYS* 3.8 13.9 + - - -
75C THR* 1.3 74.6 - - - +
77C VAL* 1.3 67.4 + - - +
78C PHE* 3.5 26.2 - - + -
108C SER* 2.7 44.0 - - - +
109C CYS* 4.8 0.2 - - - -
123C ILE* 4.2 0.2 - - - +
124C GLU* 2.8 53.9 + - + +
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Residues in contact with VAL 77 (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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75C THR* 4.0 11.2 - - + -
76C THR* 1.3 85.3 - - - +
78C PHE* 1.3 71.5 + - - +
79C VAL* 3.8 9.4 + - + +
85C PHE* 5.2 3.1 - - + -
88C VAL* 5.9 6.5 - - + -
92C TYR* 5.2 4.7 - - + -
107C ARG* 3.5 22.9 - - - +
108C SER 3.5 3.0 + - - -
109C CYS* 2.9 41.9 - - + +
110C VAL 3.3 1.6 + - - -
121C LEU* 4.9 6.1 - - + -
122C GLU 2.7 23.1 - - - +
123C ILE* 4.1 17.9 - - + -
124C GLU* 4.3 0.4 - - - -
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Residues in contact with PHE 78 (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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78A PHE* 6.2 2.5 - + - -
76B THR* 6.2 0.2 - - + -
78B PHE* 6.2 2.0 - + - -
108B SER* 4.1 12.1 - - - -
110B VAL* 3.2 38.4 - - + -
76C THR* 3.5 22.4 - - + -
77C VAL* 1.3 76.1 - - - +
79C VAL* 1.3 61.6 + - - +
108C SER 4.6 0.7 - - - -
110C VAL* 3.5 16.2 - - + -
112C VAL* 3.6 23.8 - - + -
115C LEU* 3.5 15.4 - - + +
121C LEU* 3.2 9.9 - - - +
122C GLU* 3.0 35.4 + - + +
124C GLU* 2.8 38.8 - - + -
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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
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77C VAL* 4.4 9.9 - - + +
78C PHE* 1.3 78.8 - - - +
80C LYS* 1.3 60.5 + - - +
81C ASP 4.0 9.4 - - - +
82C LEU* 3.8 25.4 - - + +
85C PHE* 3.6 33.4 - - + +
88C VAL* 5.8 5.8 - - + -
109C CYS* 5.5 0.4 - - + -
110C VAL* 2.9 18.5 + - - +
111C GLU* 3.1 21.2 - - + +
112C VAL* 3.0 26.8 + - - +
115C LEU* 4.7 0.4 - - - -
120C GLY 4.2 2.9 - - - -
121C LEU* 5.2 4.9 - - + -
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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