Contacts of the strand formed by residues 762 - 768 (chain A) in PDB entry 1KIT
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 MET 762 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A VAL* 3.4 0.9 - - - -
218A ILE* 2.8 38.5 + - - +
219A PHE* 2.6 54.4 + - + +
223A ASP* 2.8 39.3 - - + +
224A ARG* 3.8 6.7 - - - +
226A PRO* 3.1 54.1 - - + -
242A ALA* 3.9 8.3 - - + -
754A ILE* 4.4 7.0 - - + -
755A VAL 2.8 13.7 - - - +
756A GLU* 4.0 3.1 - - + -
760A SER 3.3 8.0 + - - +
761A ASN* 1.3 69.9 - - - +
763A ARG* 1.3 57.6 + - - +
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Residues in contact with ARG 763 (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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88A GLN* 4.1 11.1 + - - +
92A PHE* 3.0 48.6 - - + -
215A GLY* 3.0 39.5 + - - +
216A ASP 3.3 3.4 - - - -
217A VAL* 3.4 30.7 - - + +
220A ARG* 5.7 1.4 - - - +
753A VAL 3.6 0.7 - - - +
754A ILE* 3.3 5.9 - - - +
755A VAL* 2.8 34.1 + - + +
757A THR* 3.2 24.9 + - + +
758A ASP* 3.1 25.1 + - - -
761A ASN* 3.8 2.4 + - - +
762A MET* 1.3 74.4 - - - +
764A ILE* 1.3 63.0 + - - +
765A LEU* 5.1 2.9 - - + -
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Residues in contact with ILE 764 (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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214A GLN* 3.3 7.3 - - - +
215A GLY* 3.0 21.7 - - - -
216A ASP* 2.9 20.4 + - + +
218A ILE* 3.5 32.8 - - + -
228A ILE* 4.5 6.3 - - + -
269A GLY 4.4 9.4 - - - +
272A TRP* 3.6 34.3 - - + +
752A ILE* 4.0 23.1 - - + -
753A VAL 3.1 5.2 - - - +
754A ILE* 4.2 19.3 - - + -
763A ARG* 1.3 73.8 - - - +
765A LEU* 1.3 67.7 + - - +
766A ARG* 4.4 9.3 - - + +
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Residues in contact with LEU 765 (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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92A PHE* 4.2 17.7 - - + +
214A GLN* 3.3 10.1 - - + +
215A GLY* 4.2 16.4 - - - +
715A LEU* 5.0 0.4 - - + -
733A LEU* 3.7 45.5 - - + +
734A VAL* 4.6 9.6 - - + -
751A ALA 3.6 1.2 - - - +
752A ILE* 3.3 4.3 - - - +
753A VAL* 2.5 63.8 + - + +
755A VAL* 4.4 13.2 - - + -
763A ARG* 5.1 1.3 - - + -
764A ILE* 1.3 83.9 - - - +
766A ARG* 1.3 62.8 + - - +
767A MET* 4.2 12.1 - - - -
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Residues in contact with ARG 766 (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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95A ARG* 4.1 10.6 + - - +
212A GLU* 2.6 35.6 + - - +
214A GLN* 2.8 25.6 + - - +
267A ASP 4.1 0.8 + - - -
268A GLY* 2.9 40.5 + - - -
269A GLY 4.1 12.6 - - - -
270A ILE* 3.4 25.7 - - - +
746A LEU* 4.3 12.3 - - + +
750A ASN* 3.8 14.8 + - - +
751A ALA 3.7 4.0 - - - -
752A ILE* 4.6 5.2 - - + +
764A ILE* 4.4 11.9 - - + +
765A LEU* 1.3 74.5 - - - +
767A MET* 1.3 62.0 + - - +
768A PRO* 3.4 8.3 - - - +
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Residues in contact with MET 767 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A PHE 5.9 0.7 - - - +
159A VAL* 6.5 0.2 - - + -
161A LEU* 4.2 14.8 - - + -
214A GLN* 4.1 16.2 - - - -
717A LEU* 5.7 3.1 - - + -
733A LEU* 3.4 40.6 - - + -
743A ILE* 6.3 0.2 - - + -
750A ASN* 2.8 15.9 + - - -
751A ALA* 2.9 37.2 + - + +
753A VAL* 4.1 22.0 - - + -
765A LEU* 4.2 16.2 - - + -
766A ARG* 1.3 71.2 - - - +
768A PRO* 1.3 67.6 - - + +
769A ILE* 3.3 20.3 + - + -
772A LEU* 3.9 18.6 - - + -
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Residues in contact with PRO 768 (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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95A ARG* 3.6 37.0 - - + +
159A VAL* 4.7 15.0 - - + -
214A GLN* 5.0 2.9 - - - +
749A GLU* 3.6 5.2 - - + +
750A ASN* 3.3 7.4 - - - +
766A ARG 3.4 9.0 - - - +
767A MET* 1.3 87.9 - - + +
769A ILE* 1.3 56.5 + - - +
770A THR* 3.2 3.4 - - + -
771A LEU* 3.3 19.2 + - + -
772A LEU* 2.8 50.9 + - + +
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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