Contacts of the strand formed by residues 121 - 130 (chain E) in PDB entry 1QK1
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 121 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116E PHE* 3.6 31.6 - - + -
117E ASP 3.2 7.9 + - - +
118E GLU* 3.9 19.0 - - - +
120E TYR* 1.3 76.8 - - - +
122E LEU* 1.3 63.3 + - - +
123E SER 3.6 14.8 - - - +
238E GLY* 3.4 26.2 - - - +
239E GLY* 3.8 10.1 - - - -
290E VAL* 3.9 16.8 - - + -
291E HIS 3.5 2.9 - - - -
292E ILE* 4.0 21.1 - - + -
352E VAL* 4.3 6.3 - - + -
356E ILE* 4.3 3.6 - - + -
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Residues in contact with LEU 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E GLU 5.4 4.7 - - - +
119E ARG 6.0 0.4 - - - -
120E TYR* 4.4 7.6 - - - +
121E VAL* 1.3 75.0 - - - +
123E SER* 1.3 55.4 + - - +
237E LYS* 3.6 7.1 - - - +
238E GLY* 2.7 23.3 + - - -
291E HIS* 2.8 24.0 + - + +
293E LYS* 4.1 29.2 - - + +
328E VAL* 3.9 29.8 - - + -
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Residues in contact with SER 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E VAL* 3.6 1.2 - - - +
122E LEU* 1.3 80.9 - - - +
124E SER* 1.3 60.4 + - - +
236E GLU 3.5 13.2 - - - -
237E LYS* 4.2 7.0 - - - -
238E GLY 3.2 11.6 + - - -
290E VAL* 3.2 9.2 - - - +
291E HIS* 3.0 51.9 + - - +
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Residues in contact with SER 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E PHE* 4.2 1.2 - - - -
123E SER* 1.3 74.8 + - - +
125E ARG* 1.3 63.0 + - - +
235E MET* 3.4 2.1 - - - +
236E GLU* 3.0 32.1 + - - +
238E GLY 3.2 15.5 + - - -
239E GLY* 3.4 15.5 - - - -
240E ASN 4.8 0.9 - - - -
241E MET* 4.2 21.4 + - - -
244E VAL* 4.0 19.6 - - - +
289E GLY 3.6 4.5 - - - -
290E VAL* 3.8 10.2 - - - +
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Residues in contact with ARG 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E SER* 1.3 77.6 - - - +
126E VAL* 1.3 65.7 + - - +
127E ARG* 3.7 15.2 - - - +
221E LEU* 6.1 0.2 - - - +
223E TRP* 6.2 1.0 - - - -
233E ILE* 3.7 35.6 - - - +
234E SER 3.2 11.7 - - - +
235E MET* 3.8 24.8 - - + +
241E MET* 4.3 1.5 - - - +
244E VAL* 4.2 1.6 - - - -
287E ARG* 3.7 15.4 + - - +
288E ALA* 3.4 2.1 - - - -
289E GLY* 2.8 43.3 + - - +
400E PO4 2.7 47.3 + - - -
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Residues in contact with VAL 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ARG* 1.3 80.5 - - - +
127E ARG* 1.3 63.5 + - - +
233E ILE* 3.5 3.3 - - - +
234E SER 2.9 31.5 + - - +
241E MET* 3.8 22.4 - - - -
244E VAL* 3.9 14.4 - - + -
245E PHE* 4.4 16.6 - - + -
248E PHE* 3.7 34.6 - - + -
286E LEU* 3.7 26.2 - - + -
287E ARG 3.5 3.6 - - - +
288E ALA* 4.1 9.9 - - + -
345E VAL* 4.8 1.1 - - + -
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Residues in contact with ARG 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ARG* 3.7 17.9 - - - +
126E VAL* 1.3 76.7 - - - +
128E THR* 1.3 73.0 + - - +
231E ARG* 3.7 24.2 - - + +
232E VAL 3.4 8.5 - - - +
233E ILE* 4.0 13.7 - - + -
248E PHE* 4.2 2.5 - - - -
276E LEU* 5.8 0.8 - - - +
281E ASN* 2.8 31.7 + - - -
285E GLY* 3.0 28.6 + - - +
286E LEU* 3.2 9.0 - - - +
287E ARG* 3.0 53.3 + - - +
336E ARG* 4.2 7.9 - - - +
400E PO4 2.8 53.8 + - - +
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Residues in contact with THR 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ARG* 1.3 85.7 - - - +
129E GLY* 1.3 62.6 + - - +
130E ARG* 3.0 23.1 + - - +
231E ARG* 3.3 6.6 - - - +
232E VAL* 2.8 41.8 + - + -
248E PHE* 3.5 29.2 - - + -
252E LEU* 4.0 11.0 - - + -
284E THR 2.7 27.2 + - - -
285E GLY* 3.3 9.9 + - - -
286E LEU* 4.6 1.6 - - - -
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Residues in contact with GLY 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ARG* 5.7 0.2 - - - +
128E THR* 1.3 79.2 + - - +
130E ARG* 1.3 89.1 + - - -
230E THR 3.2 12.3 - - - -
231E ARG* 4.3 7.2 - - - -
232E VAL* 4.6 1.3 - - - -
274E TYR* 4.7 2.1 - - - +
276E LEU* 3.5 29.8 - - - +
285E GLY 4.2 2.6 + - - -
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Residues in contact with ARG 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 4.4 10.5 - - - +
128E THR* 3.0 25.6 + - + +
129E GLY* 1.3 101.8 + - - +
131E SER* 1.3 62.2 + - - +
132E ILE* 5.5 1.1 - - + +
229E HIS* 3.4 5.4 + - - +
230E THR* 3.0 42.8 + - - +
232E VAL* 5.0 4.5 - - + -
248E PHE* 5.5 0.8 - - - -
252E LEU* 3.7 34.4 - - + +
266E PHE* 3.7 48.3 - - + -
274E TYR* 3.3 57.5 + - - +
276E LEU* 3.6 4.7 - - - +
284E THR 4.2 2.0 + - - -
341E GLU* 4.6 7.1 + - - -
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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