Contacts of the strand formed by residues 76 - 83 (chain A) in PDB entry 3N51
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 GLU 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.6 25.9 + - - +
55A ARG* 4.3 8.6 + - - -
67A LEU* 4.0 26.4 - - + +
68A CYS 3.3 6.5 - - - +
69A LYS* 4.1 16.4 + - - +
74A GLY 3.2 5.2 + - - +
75A GLN* 1.3 98.6 + - - +
77A CYS* 1.3 62.0 + - - +
115A TYR* 5.3 1.9 - - - -
129A GLU* 5.7 0.2 - - - -
130A VAL* 4.6 14.1 + - + +
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Residues in contact with CYS 77 (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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51A TYR* 3.4 39.9 - - - -
67A LEU* 3.5 6.2 - - - +
68A CYS* 2.8 42.0 + - - +
75A GLN* 4.6 4.7 - - + +
76A GLU* 1.3 76.9 - - - +
78A ALA* 1.3 60.1 + - - +
79A VAL* 4.3 2.0 - - - -
115A TYR* 4.5 8.7 - - + -
127A VAL* 3.5 17.7 - - + -
128A GLY 3.2 15.3 - - - +
129A GLU* 5.1 0.4 - - - +
130A VAL* 4.1 11.0 - - - +
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Residues in contact with ALA 78 (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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57A LEU* 3.9 22.2 - - + -
65A VAL* 4.1 0.7 - - + -
66A ILE 3.5 4.0 - - - -
77A CYS* 1.3 74.2 - - - +
79A VAL* 1.3 63.9 + - - +
127A VAL* 4.1 0.3 - - - +
128A GLY 2.8 33.5 + - - +
130A VAL* 3.9 14.8 - - + +
701A BK3 3.3 34.9 - - + +
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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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47A PHE* 3.6 39.5 - - + -
64A GLU 3.5 2.1 - - - +
65A VAL* 3.3 2.6 - - - -
66A ILE* 2.8 41.4 + - + +
68A CYS* 4.0 20.0 - - + -
77A CYS* 4.3 1.3 - - - -
78A ALA* 1.3 80.3 - - - +
80A LYS* 1.3 70.7 + - - +
81A VAL* 4.2 9.0 - - + -
125A TYR* 4.0 13.5 - - + -
126A LEU 3.4 9.2 - - - +
127A VAL* 3.7 18.6 - - + -
701A BK3 3.8 3.6 - - - -
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Residues in contact with LYS 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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60A GLY* 4.1 1.6 - - - -
61A SER 2.7 37.6 + - - +
63A GLY 4.3 7.4 - - - +
64A GLU 3.5 5.4 - - - +
65A VAL* 3.8 24.0 - - + -
79A VAL* 1.3 71.2 - - - +
81A VAL* 1.3 61.9 + - - +
82A ILE* 3.9 18.0 + - + +
124A PHE 3.6 1.7 - - - +
125A TYR* 3.5 3.3 - - - -
126A LEU* 2.9 35.7 + - + +
194A ILE* 5.6 1.2 - - - +
195A ASP* 2.7 35.3 + - - -
198A LEU* 4.1 15.7 - - + +
701A BK3 3.5 35.6 - - + +
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Residues in contact with VAL 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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47A PHE* 5.9 1.6 - - + -
63A GLY* 3.4 6.4 - - - -
64A GLU* 2.9 34.4 + - + +
66A ILE* 3.9 22.0 - - + -
79A VAL* 4.2 7.9 - - + -
80A LYS* 1.3 74.4 - - - +
82A ILE* 1.3 61.6 + - - +
83A SER 4.0 1.6 + - - -
123A TYR* 3.5 39.7 - - + -
124A PHE 3.4 3.8 - - - +
125A TYR* 3.8 25.6 - - + -
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Residues in contact with ILE 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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62A PHE* 3.7 31.9 - - + +
80A LYS* 4.2 15.5 - - + +
81A VAL* 1.3 74.0 - - - +
83A SER* 1.3 64.6 + - - +
84A LYS* 3.3 1.5 + - - -
87A VAL* 3.9 25.1 - - + +
123A TYR* 3.3 4.6 - - - -
124A PHE* 2.9 48.2 + - + +
126A LEU* 3.7 28.7 - - + -
198A LEU* 5.0 2.2 - - + -
202A PHE* 3.9 34.8 - - + -
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Residues in contact with SER 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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62A PHE 4.5 3.4 + - - -
63A GLY* 5.7 0.4 - - - -
81A VAL 4.0 2.4 + - - -
82A ILE* 1.3 70.2 - - - +
84A LYS* 1.3 54.1 + - - +
85A ARG* 3.5 19.8 + - - +
86A GLN* 3.2 34.0 + - - +
87A VAL* 2.7 38.7 + - - +
122A GLY 3.6 1.4 + - - -
123A TYR* 3.5 28.8 - - - -
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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