Contacts of the strand formed by residues 78 - 83 (chain G) in PDB entry 1N9S
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 VAL 78 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 3.4 19.0 + - + +
77A ASN* 2.8 15.7 + - - +
29G VAL* 4.0 18.4 - - + -
30G LYS 3.8 8.5 - - - +
31G LEU* 4.6 0.7 - - + -
32G LYS* 4.2 3.3 - - - +
49G PHE* 4.9 6.5 - - + +
51G LEU* 5.1 4.3 - - + -
73G ILE* 4.0 15.5 - - + -
74G ARG 3.4 16.2 - - - +
75G SER* 2.6 30.2 + - - +
76G ASN 3.2 1.8 - - - +
77G ASN* 1.3 74.5 - - - +
79G LEU* 1.3 63.8 + - - +
80G TYR* 3.6 19.7 - - - +
81G ILE* 4.2 11.4 - - + -
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Residues in contact with LEU 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.8 13.2 - - + -
33A PHE* 3.7 26.2 - - + -
38A TYR* 3.1 26.7 - - + +
73A ILE* 3.9 2.4 - - + +
74A ARG 3.1 22.7 + - - -
77A ASN* 3.0 43.9 + - + +
30G LYS* 2.9 27.1 + - + +
31G LEU 3.9 15.3 - - - +
32G LYS* 4.0 1.7 - - - +
77G ASN 3.8 1.8 + - - -
78G VAL* 1.3 74.0 - - - +
80G TYR* 1.3 81.3 + - + +
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Residues in contact with TYR 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.1 42.2 - + - -
58A GLU* 4.6 5.0 + - - -
68A LEU* 3.7 27.3 - - + +
71A ILE* 4.4 13.5 - - + -
72A PHE 3.4 16.4 - - - +
73A ILE* 4.0 11.7 - - + -
74A ARG* 4.8 0.7 - - - +
28G GLY 3.6 0.4 - - - +
29G VAL* 3.7 0.7 - - - -
30G LYS* 2.9 53.2 + - + +
37G GLU* 4.7 3.7 + - - -
78G VAL* 3.6 2.5 - - - +
79G LEU* 1.3 98.8 - - + +
81G ILE* 1.3 77.2 + - - +
82G ARG* 4.2 23.7 - - + -
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Residues in contact with ILE 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 3.3 2.8 - - - -
72A PHE* 2.9 38.2 + - + +
19G LEU* 4.3 14.4 - - + -
22G LEU* 4.2 14.8 - - + -
27G VAL* 4.1 23.1 - - + -
28G GLY 3.2 8.5 - - - +
29G VAL* 4.7 5.8 - - + -
42G LEU* 5.6 3.4 - - + -
49G PHE* 3.4 28.9 - - + -
51G LEU* 3.7 27.6 - - + -
78G VAL* 4.2 7.0 - - + -
80G TYR* 1.3 86.7 - - - +
82G ARG* 1.3 64.0 + - - +
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Residues in contact with ARG 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A THR 5.8 0.6 + - - -
68A LEU* 4.5 25.5 - - - +
69A GLY 5.2 3.4 - - - +
70A GLU 3.4 15.3 - - - +
71A ILE* 4.0 11.4 - - + -
72A PHE* 5.3 0.7 - - - -
22G LEU* 5.2 1.3 - - - -
27G VAL* 2.8 12.0 - - - +
28G GLY* 2.5 48.2 + - - +
37G GLU* 2.8 36.3 + - - -
39G ARG* 3.9 15.2 - - - +
80G TYR* 4.2 13.4 + - + -
81G ILE* 1.3 76.2 - - - +
83G GLU* 1.3 61.8 + - - +
84G LEU* 3.4 24.0 - - + +
85G PRO* 4.5 14.5 - - - +
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Residues in contact with GLU 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLY* 5.2 8.3 - - - -
70A GLU* 3.6 24.4 + - + +
72A PHE* 6.1 0.2 - - + -
22G LEU* 4.0 22.0 - - + +
25G HIS* 3.7 25.0 - - + -
26G ARG 3.6 7.9 - - - +
27G VAL* 4.2 4.3 - - - +
82G ARG* 1.3 75.4 - - - +
84G LEU* 1.3 75.6 + - - +
85G PRO* 3.4 8.0 - - - +
86G ASN 5.5 1.6 - - - +
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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