Contacts of the strand formed by residues 125 - 129 (chain A) in PDB entry 2FK8
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 ARG 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A VAL* 4.2 9.2 - - + -
99A VAL* 3.4 24.0 - - + -
116A LEU* 2.9 49.9 + - + +
117A ALA* 3.1 23.0 + - - +
119A ILE* 3.4 13.9 + - + +
121A THR* 3.5 35.0 + - - +
122A ASN 4.9 0.6 - - - -
123A ARG* 3.0 31.6 + - - -
124A SER* 1.3 75.9 + - - +
126A GLN* 1.3 61.9 + - - +
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Residues in contact with GLN 126 (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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99A VAL 3.0 10.2 + - - +
100A ILE* 3.2 26.4 - - + +
101A GLY 2.8 22.9 + - - -
116A LEU* 4.0 8.3 - - - +
124A SER* 5.5 3.4 - - - +
125A ARG* 1.3 76.1 - - - +
127A VAL* 1.3 64.4 + - - +
128A LEU* 3.7 35.8 - - + +
135A PHE* 5.7 0.7 - - - -
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Residues in contact with VAL 127 (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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82A CYS* 3.8 18.4 - - - -
88A MET* 4.7 0.9 - - + -
101A GLY 3.4 10.1 - - - +
103A THR* 4.2 9.2 - - + -
109A HIS* 3.1 35.9 + - + +
112A CYS* 3.7 21.1 - - + -
113A GLU* 3.7 39.2 - - + +
116A LEU* 4.0 8.1 - - + -
126A GLN* 1.3 75.7 - - - +
128A LEU* 1.3 68.8 + - - +
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Residues in contact with LEU 128 (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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100A ILE* 4.1 9.9 - - + -
101A GLY 2.8 14.3 + - - +
102A LEU* 3.5 9.3 - - + -
103A THR* 3.2 20.8 + - - +
109A HIS* 3.8 3.8 - - - -
126A GLN* 3.7 32.1 - - + +
127A VAL* 1.3 81.2 - - - +
129A LEU* 1.3 59.6 + - - +
130A GLN* 3.1 38.7 + - - +
135A PHE* 4.0 22.9 - - + -
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Residues in contact with LEU 129 (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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103A THR 3.3 13.9 - - - +
104A LEU* 3.6 12.3 - - - +
105A SER 3.4 34.8 - - - +
106A LYS* 3.7 19.3 - - + +
109A HIS* 3.6 24.4 + - + +
128A LEU* 1.3 70.0 - - - +
130A GLN* 1.3 61.3 + - - +
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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