Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 1U31
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 LYS 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ASN 2.9 16.6 + - - +
47A SER* 3.5 14.3 - - - -
48A ILE 2.7 34.1 + - - +
76A GLY 3.9 1.6 + - - +
77A LYS* 1.3 68.2 - - - +
79A VAL* 1.3 56.0 + - - +
80A ARG* 4.6 29.2 - - + +
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Residues in contact with VAL 79 (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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48A ILE* 3.5 20.6 - - + -
50A ILE* 4.0 13.5 - - + -
69A VAL* 3.7 36.7 - - + +
72A LEU* 3.7 32.5 - - + -
73A THR* 4.1 11.1 + - - +
77A LYS* 3.4 19.9 + - + +
78A LYS* 1.3 75.8 - - - +
80A ARG* 1.3 69.3 + - - +
107A ILE* 3.7 23.2 - - - +
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Residues in contact with ARG 80 (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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48A ILE 3.0 7.1 + - - +
49A ILE* 3.4 28.1 - - + +
50A ILE* 2.8 34.3 + - - +
78A LYS* 4.6 25.7 - - + +
79A VAL* 1.3 82.6 - - - +
81A PHE* 1.3 60.4 + - - +
106A ASP 5.6 0.4 - - - -
107A ILE* 3.5 22.4 - - + +
109A LEU* 3.5 32.8 - - + +
114A ILE* 3.9 18.2 - - + +
117A ASP* 2.9 39.6 + - - +
121A THR* 5.0 1.6 + - - -
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Residues in contact with PHE 81 (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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50A ILE* 3.2 36.8 - - + +
52A PRO* 4.1 6.7 - - + -
56A LEU* 5.7 0.2 - - + -
65A ILE* 4.2 14.1 - - + -
69A VAL* 3.6 33.7 - - + -
80A ARG* 1.3 77.4 - - - +
82A GLY* 1.3 58.5 + - - +
83A ILE* 3.7 17.0 - - + -
98A LEU* 3.7 34.1 - - + -
103A VAL* 3.5 37.0 - - + -
107A ILE* 2.8 22.5 + - + +
108A VAL* 4.3 3.4 - - + -
109A LEU 3.1 24.3 + - - +
114A ILE* 3.4 11.1 - - - +
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Residues in contact with GLY 82 (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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49A ILE* 4.2 6.9 - - - +
50A ILE 2.7 13.2 + - - -
51A THR* 3.6 20.9 - - - -
52A PRO* 3.6 5.2 - - - +
81A PHE* 1.3 72.9 - - - +
83A ILE* 1.3 61.9 + - - -
84A HIS 3.9 0.3 + - - -
109A LEU 3.6 2.9 - - - -
114A ILE* 3.8 21.5 - - - -
151A LEU* 3.7 16.7 - - - +
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Residues in contact with ILE 83 (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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52A PRO* 4.6 6.3 - - + -
81A PHE* 3.7 19.3 - - + -
82A GLY* 1.3 77.5 - - - +
84A HIS* 1.3 73.9 + - - +
85A PRO* 3.7 1.5 - - + +
87A ALA* 4.9 2.0 - - + -
92A GLY* 5.8 2.5 - - - +
94A LEU* 4.1 26.0 - - + -
95A ASN* 3.4 24.2 - - - +
98A LEU* 3.9 8.5 - - + -
108A VAL* 3.6 28.9 - - + -
109A LEU 2.9 18.3 + - - +
110A GLU* 3.6 17.8 - - - +
111A MET* 2.8 30.2 + - - +
151A LEU* 4.5 0.2 - - - -
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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