Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 3NTY
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 PHE 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.3 11.4 - - + -
14A HIS* 5.4 2.0 - - + -
15A PHE 3.0 29.2 - - - -
16A MET* 3.7 32.3 - - + -
17A PRO* 3.5 25.1 - - + -
47A ARG 2.6 12.0 + - - +
48A HIS* 3.1 19.7 - + - -
49A ILE 2.7 33.3 + - - +
78A ASP 4.0 0.4 + - - -
79A ILE* 1.3 70.2 - - - +
81A TYR* 1.3 57.0 + - - +
82A THR* 3.6 18.4 - - - -
112A ASP* 3.5 23.6 - - + -
113A LEU* 3.8 22.0 - - + -
162A SER* 5.0 1.8 - - - -
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Residues in contact with TYR 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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49A ILE* 3.5 11.4 - - + +
51A SER* 2.9 36.7 + - - -
58A GLU* 3.2 17.7 + - - +
61A VAL* 3.9 15.9 - - + -
65A ILE* 3.9 28.5 - - + -
76A ARG* 4.3 7.2 - - - +
79A ILE* 3.9 5.6 - - + -
80A PHE* 1.3 73.8 - - - +
82A THR* 1.3 76.8 + - - +
83A SER* 4.0 2.2 - - - -
106A LEU* 3.4 35.2 - - + +
108A LEU* 4.5 6.3 - - + -
111A VAL* 3.7 22.9 - - + +
112A ASP* 2.8 43.8 + - - +
113A LEU 3.3 4.3 + - - -
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Residues in contact with THR 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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48A HIS* 3.8 9.5 + - - -
49A ILE 3.0 11.7 + - - -
50A ASP* 3.2 25.8 - - - +
51A SER 2.7 29.2 + - - +
80A PHE* 3.6 9.7 - - - -
81A TYR* 1.3 84.9 - - - +
83A SER* 1.3 70.3 + - - +
84A LYS* 4.5 0.4 - - + -
113A LEU* 3.4 38.6 - - + +
115A LEU* 4.1 14.4 - - + -
190A GLN* 5.0 1.1 - - - +
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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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51A SER 3.0 5.6 - - - -
52A ALA* 4.2 2.1 - - - -
58A GLU* 3.0 25.5 + - - -
81A TYR* 4.0 1.7 + - - -
82A THR* 1.3 75.7 - - - +
84A LYS* 1.3 73.8 + - - +
102A SER* 3.7 12.2 + - - -
111A VAL* 3.7 20.9 - - - -
113A LEU 2.9 6.9 + - - +
114A TYR* 3.3 23.6 - - - -
115A LEU 3.0 21.1 + - - -
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Residues in contact with LYS 84 (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 ASP* 2.5 43.1 + - - -
51A SER 3.7 5.2 + - - +
52A ALA* 3.2 14.5 - - + +
53A HIS* 3.4 22.5 + - - +
55A TYR* 3.0 21.8 + - - -
82A THR* 4.5 0.4 - - + -
83A SER* 1.3 85.5 + - - +
85A LEU* 1.3 63.0 + - - +
86A TRP* 3.6 3.1 + - - +
102A SER* 5.2 0.3 + - - -
114A TYR* 3.8 7.4 + - - -
115A LEU* 3.2 29.6 - - + +
117A HIS* 3.5 34.2 + - + +
166A SER* 4.8 0.4 - - - +
190A GLN* 3.5 23.1 + - - +
351A NAP 3.8 8.3 - - - +
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Residues in contact with LEU 85 (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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84A LYS* 1.3 69.6 - - - +
86A TRP* 1.3 68.3 + - - +
89A SER* 3.8 24.2 - - - +
90A HIS* 4.4 8.6 + - + -
95A VAL* 4.1 20.4 - - + +
98A ALA* 3.6 22.2 - - + -
114A TYR* 3.5 30.2 - - + +
115A LEU 2.6 16.2 + - - +
116A ILE* 4.3 12.1 - - + -
117A HIS* 3.1 23.7 + - - +
147A THR* 3.7 30.1 - - + -
151A VAL* 4.3 2.5 - - + -
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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