Contacts of the strand formed by residues 121 - 125 (chain A) in PDB entry 2V5Y
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 ASN 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A HIS* 3.2 8.3 - - - -
81A TYR* 3.0 68.6 + - + +
82A PHE* 5.6 0.4 - - - +
117A THR* 4.1 9.3 + - - +
119A THR* 3.0 33.3 + - - -
120A TRP* 1.3 79.0 + - - +
122A ARG* 1.3 65.6 + - - +
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Residues in contact with ARG 122 (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 ASP* 3.1 37.4 + - - +
79A PHE 3.5 4.7 - - - +
80A HIS* 3.3 35.7 + - + +
81A TYR* 4.2 4.0 + - - -
121A ASN* 1.3 75.9 - - - +
123A ALA* 1.3 65.8 + - - +
124A GLU* 2.7 38.5 + - - +
156A LYS* 4.5 4.6 - - - +
163A THR* 4.0 2.4 + - - +
164A ARG* 3.1 48.0 - - - +
246A GLY* 4.7 7.6 + - - +
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Residues in contact with ALA 123 (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 ASP* 3.3 2.7 - - - -
79A PHE* 2.9 61.6 + - + +
81A TYR* 4.1 4.7 - - + -
110A TRP* 3.9 26.7 - - + +
122A ARG* 1.3 79.0 - - - +
124A GLU* 1.3 59.5 + - - +
125A LEU* 5.7 0.2 - - + -
246A GLY 3.8 10.3 - - - -
247A GLY* 5.4 0.2 - - - -
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Residues in contact with GLU 124 (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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76A CYS* 3.6 11.2 - - - -
77A ILE 3.1 11.9 - - - +
78A ASP* 3.7 9.6 - - + +
122A ARG* 2.7 28.4 + - - +
123A ALA* 1.3 72.0 - - - +
125A LEU* 1.3 68.9 - - - +
162A CYS* 3.2 8.9 - - - +
163A THR* 3.1 14.2 + - - +
164A ARG* 2.6 33.1 + - - -
165A THR* 3.1 19.0 + - - +
246A GLY 3.3 18.0 + - - +
247A GLY* 3.1 3.3 - - - -
248A VAL 3.0 24.1 + - - -
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Residues in contact with LEU 125 (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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75A HIS* 6.1 0.2 - - - -
76A CYS* 3.8 1.7 - - - -
77A ILE* 2.7 48.5 + - + +
79A PHE* 4.4 23.3 - - + -
96A VAL* 4.1 23.8 - - + -
109A ILE* 4.4 18.4 - - + -
110A TRP* 4.5 20.0 - - + -
124A GLU* 1.3 87.4 - - - +
126A ALA* 1.3 60.5 + - - +
127A ILE* 3.6 20.5 + - + -
137A VAL* 4.5 11.7 - - + -
139A PHE* 5.8 0.4 - - + -
162A CYS* 3.4 6.5 - - - -
248A VAL* 3.2 12.8 - - + +
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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