Contacts of the strand formed by residues 120 - 125 (chain A) in PDB entry 3QV2
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 HIS 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASN* 3.6 2.6 + - - -
74A THR* 3.4 12.1 + - + +
75A TRP 3.0 24.3 + - - -
118A PRO* 3.2 0.9 - - - +
119A LYS* 1.3 99.3 + - + +
121A ILE* 1.3 65.3 + - - +
172A ALA 3.5 4.0 - - - -
173A ARG* 3.9 8.1 - - + -
316A LEU* 3.2 28.9 - - + -
317A PHE* 3.5 40.6 - + + -
319A ASP* 2.7 37.2 + - - -
320A LEU* 3.9 19.5 - - + +
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Residues in contact with ILE 121 (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 TRP* 3.3 18.8 - - + +
77A MET* 5.3 0.9 - - + -
107A TYR* 3.4 24.0 - - + +
111A LEU* 3.8 20.4 - - + -
118A PRO* 4.0 13.5 - - + -
120A HIS* 1.3 80.1 - - - +
122A PHE* 1.3 63.4 + - - +
123A ILE* 4.1 12.8 - - + -
142A LEU* 3.8 12.6 - - + -
147A TYR* 3.7 35.0 - - + +
170A VAL 3.7 0.7 - - - +
171A MET* 3.7 0.7 - - - -
172A ALA* 2.7 44.6 + - + +
316A LEU* 3.6 8.0 - - - +
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Residues in contact with PHE 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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18A LEU* 4.5 7.4 - - + -
75A TRP 2.9 10.2 + - - +
76A PHE* 3.7 18.2 - + + -
77A MET* 3.0 29.6 + - - +
121A ILE* 1.3 75.3 - - - +
123A ILE* 1.3 74.8 + - - +
124A GLU* 4.2 8.5 - - + -
169A TYR* 3.7 28.5 - + + -
170A VAL 3.4 3.6 - - - -
171A MET* 3.9 23.3 - - + -
309A ILE* 3.6 28.3 - - + -
312A LEU* 3.8 25.8 - - + -
313A MET* 4.0 24.0 - - + -
316A LEU* 3.8 16.8 - - + -
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Residues in contact with ILE 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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77A MET* 3.2 8.7 - - + +
79A PRO* 3.9 24.9 - - + -
103A VAL* 6.0 0.2 - - + -
107A TYR* 3.1 35.2 - - + +
121A ILE* 4.1 7.9 - - + -
122A PHE* 1.3 84.1 - - - +
124A GLU* 1.3 66.2 + - - +
129A PHE* 4.3 21.1 - - + -
135A PHE* 4.8 4.3 - - + -
138A ILE* 4.5 13.2 - - + -
142A LEU* 4.9 3.1 - - + -
168A TYR 3.9 0.4 - - - +
169A TYR* 3.4 5.2 - - - -
170A VAL* 2.9 60.7 + - + +
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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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18A LEU* 4.6 2.5 - - + -
77A MET 2.9 8.5 + - - +
78A SER* 3.1 39.8 - - - -
79A PRO* 3.5 1.4 - - - +
122A PHE* 4.2 8.5 - - + -
123A ILE* 1.3 75.9 - - - +
125A ASN* 1.3 74.1 + - - +
165A ARG* 5.4 0.2 + - - -
167A ARG* 3.3 35.5 + - - +
168A TYR 3.5 3.1 - - - +
169A TYR* 3.4 29.5 + - + -
303A SER 4.8 2.5 - - - +
304A VAL* 3.7 25.2 - - + +
309A ILE* 4.2 5.2 - - + -
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Residues in contact with ASN 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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79A PRO* 2.9 42.8 + - + +
80A PRO 3.9 4.6 + - - -
81A CYS* 3.5 7.3 - - - +
84A TYR* 3.5 16.3 - - - -
123A ILE* 5.2 0.2 - - + -
124A GLU* 1.3 81.7 + - - +
126A VAL* 1.3 80.2 + - - +
129A PHE* 3.5 33.9 - - + +
167A ARG* 3.3 15.4 - - - +
168A TYR* 2.8 35.1 + - + +
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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