Contacts of the strand formed by residues 75 - 80 (chain A) in PDB entry 2P3L
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 GLY 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU* 1.3 72.5 - - - +
76A LYS* 1.3 58.4 + - - -
77A VAL 3.5 0.3 + - - -
96A ASN 2.7 16.6 + - - -
97A VAL* 3.5 3.4 - - - +
98A ARG* 2.8 48.4 + - - -
99A GLU 2.9 12.5 + - - +
141A ASP* 3.5 8.1 - - - -
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Residues in contact with LYS 76 (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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74A GLU 3.5 0.9 + - - -
75A GLY* 1.3 68.5 - - - -
77A VAL* 1.3 63.4 + - - +
78A VAL* 4.1 12.3 - - + -
98A ARG* 3.4 17.9 - - - +
99A GLU* 3.6 37.7 - - + +
101A LYS* 5.2 4.9 - - - +
125A ARG* 5.7 0.2 - - - +
138A GLU* 3.0 31.6 + - - +
139A ARG* 2.8 41.4 + - + +
140A CYS* 3.4 14.4 - - + +
141A ASP* 2.8 40.1 + - - +
142A THR 3.1 5.9 + - - -
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO* 4.3 3.8 - - + -
74A GLU 4.3 0.4 - - - +
75A GLY 4.2 1.8 - - - +
76A LYS* 1.3 72.5 - - - +
78A VAL* 1.3 67.8 + - - +
79A ASP 4.7 0.2 - - - +
91A CYS* 4.3 7.4 - - + -
97A VAL* 4.0 29.4 - - + -
99A GLU 2.7 16.8 + - - +
100A VAL* 3.4 13.9 - - + +
101A LYS 2.8 27.5 + - - +
142A THR* 3.4 33.7 - - + +
144A LEU* 3.8 31.6 - - + -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 4.1 17.9 + - - -
77A VAL* 1.3 77.5 - - - +
79A ASP* 1.3 57.5 + - - +
80A LEU* 3.5 27.4 - - + -
101A LYS* 3.3 15.3 - - + +
103A LEU* 4.6 6.1 - - + -
138A GLU* 5.0 3.1 - - + +
139A ARG 5.0 0.2 - - - +
140A CYS* 3.7 20.2 - - + -
142A THR 3.0 9.0 + - - +
143A LEU* 3.7 13.8 - - + +
144A LEU* 2.8 34.0 + - - +
171A TRP* 3.6 26.5 - - + -
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Residues in contact with ASP 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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77A VAL* 4.1 0.4 + - + -
78A VAL* 1.3 71.4 - - - +
80A LEU* 1.3 69.2 + - - +
81A GLY 3.5 1.7 + - - +
82A CYS* 3.4 21.1 - - - +
87A TRP* 3.5 22.9 + - - +
88A SER* 2.9 39.9 + - - +
100A VAL* 4.8 4.7 - - + -
101A LYS 2.8 12.1 + - - +
102A GLY* 3.3 1.5 - - - -
103A LEU* 2.9 28.6 + - - +
144A LEU* 3.6 23.0 - - + +
146A ASP* 5.1 0.7 + - - +
1001A SAH 5.1 1.0 + - - -
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Residues in contact with LEU 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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78A VAL* 3.5 25.4 - - + -
79A ASP* 1.3 70.8 + - - +
81A GLY* 1.3 62.3 + - - +
103A LEU* 4.0 11.7 - - + -
132A VAL* 4.2 23.8 - - + -
143A LEU* 3.8 30.7 - - + -
144A LEU 2.8 13.6 + - - +
145A CYS* 3.4 15.4 - - - -
146A ASP 3.3 24.8 + - - -
147A ILE* 3.8 7.8 - - + +
167A LEU* 4.1 19.3 - - + -
168A VAL* 4.6 2.0 - - + -
171A TRP* 4.2 23.3 - - + +
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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