Contacts of the strand formed by residues 122 - 125 (chain A) in PDB entry 2Z1Z
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 VAL 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLN* 2.9 17.7 - - - +
104A ARG* 3.1 43.6 - - + +
107A ILE* 3.6 32.8 - - + -
108A ALA* 4.0 9.9 - - + +
117A ILE* 4.0 13.7 - - + -
118A GLY 3.9 14.1 - - - +
119A ASP 3.5 5.8 + - - +
120A ASP 3.4 0.6 - - - -
121A ASP* 1.3 79.8 - - - +
123A PHE* 1.3 64.0 + - - +
124A VAL 4.0 0.4 - - - +
281A TRP* 4.0 19.7 - - + -
282A THR 3.7 3.1 - - - -
283A VAL* 4.4 6.3 - - + +
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Residues in contact with PHE 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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98A GLN* 3.2 41.5 - - + -
120A ASP 4.2 5.6 - - - -
121A ASP* 3.4 24.9 - - - -
122A VAL* 1.3 72.5 - - - +
124A VAL* 1.3 62.8 + - - +
125A SER 3.8 0.2 + - - -
131A ASP* 4.6 1.9 - - - +
281A TRP* 2.9 7.6 - - - -
282A THR* 2.8 42.7 + - - +
284A ILE* 4.2 18.8 - - + -
297A ALA* 4.1 21.8 - - + -
300A PHE* 3.5 40.4 - + + -
301A ASN* 3.5 23.3 - - + -
304A ILE* 4.8 9.4 - - + -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU 3.7 9.9 - - - +
98A GLN* 2.9 18.2 + - - +
99A GLY* 3.8 8.9 + - - -
103A LEU* 3.7 26.0 - - + -
104A ARG* 3.9 18.4 - - + +
107A ILE* 4.1 17.3 - - + -
122A VAL* 4.7 1.1 - - + -
123A PHE* 1.3 73.1 - - - +
125A SER* 1.3 63.6 + - - +
279A LEU* 3.5 37.5 - - + -
280A GLY 3.4 3.6 - - - -
281A TRP* 4.0 0.2 - - - -
304A ILE* 6.0 0.2 - - - +
308A PHE* 3.5 15.9 - - - -
311A ALA* 4.1 10.1 + - + +
316A GLN* 4.2 4.5 - - + -
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Residues in contact with SER 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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123A PHE 4.6 0.7 - - - -
124A VAL* 1.3 77.3 - - - +
126A ASP* 1.3 60.1 + - - +
127A GLY 3.1 12.3 + - - -
131A ASP* 2.8 40.4 + - - -
134A ARG* 3.8 15.3 - - - -
279A LEU* 3.2 7.4 - - - +
280A GLY 2.9 30.0 + - - -
308A PHE* 3.8 8.1 - - - -
311A ALA* 3.6 12.4 - - - +
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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