Contacts of the strand formed by residues 68 - 72 (chain A) in PDB entry 7NG0
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 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.4 1.1 - - + -
36A ILE* 3.9 15.0 - - + -
66A GLN 4.7 0.2 - - - +
67A PRO* 1.3 73.1 - - + +
69A VAL* 1.3 59.3 + - - +
70A VAL* 3.7 22.4 - - + -
80A ILE* 4.8 6.5 - - + -
82A ALA 3.7 9.9 - - - +
83A GLY 3.8 7.2 - - - +
86A ARG* 3.7 31.9 - - + +
87A TRP* 4.8 4.9 - - + -
98A ILE* 3.4 44.9 - - + -
99A PRO 2.9 17.3 + - - +
100A ALA* 3.0 32.2 - - + +
101A ILE 3.1 4.3 + - - -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO 3.8 6.7 + - - +
68A ILE* 1.3 72.1 - - - +
70A VAL* 1.3 61.9 + - - +
80A ILE* 3.7 0.9 - - - +
81A ILE* 2.8 51.8 + - + -
82A ALA* 3.0 28.3 + - + +
86A ARG* 4.7 1.3 - - - +
101A ILE* 3.7 31.0 - - + +
103A LYS* 5.0 9.9 - - + -
105A LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.9 15.3 - - + -
36A ILE* 4.6 1.6 - - + -
68A ILE* 3.7 26.5 - - + -
69A VAL* 1.3 81.8 - - - +
71A ARG* 1.3 59.6 + - - +
78A PHE* 4.0 14.8 - - + -
79A GLU 3.3 10.8 - - - +
80A ILE* 3.9 17.3 - - + +
81A ILE* 3.8 7.4 - - - +
100A ALA* 3.8 22.0 - - + -
101A ILE 3.1 18.2 + - - +
102A ILE* 3.3 15.9 - - + -
103A LYS* 3.2 14.9 + - - +
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 1.3 75.1 - - - +
72A GLU* 1.3 74.1 + - - +
73A CYS* 3.8 23.2 + - - +
78A PHE* 3.3 7.3 - - - +
79A GLU* 2.9 63.9 + - + +
81A ILE* 3.9 10.9 - - + +
102A ILE* 5.2 1.6 - - - +
103A LYS 3.4 21.8 - - - +
105A LEU* 3.0 27.4 + - + +
106A ASN* 3.7 1.6 - - - +
107A ASP* 3.0 40.3 + - - +
110A THR* 3.5 19.1 - - + +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 5.8 2.0 + - - -
71A ARG* 1.3 83.6 + - - +
73A CYS* 1.3 64.4 + - - +
74A GLY* 3.1 20.2 + - - +
76A GLY* 4.5 6.6 + - - -
77A ARG 3.6 4.7 - - - -
78A PHE* 3.4 28.9 - - + -
102A ILE* 4.2 27.8 - - + +
103A LYS 4.6 1.4 + - - -
104A ASN* 5.9 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