Contacts of the strand formed by residues 857 - 864 (chain A) in PDB entry 5C58
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 857 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A GLY* 3.2 3.1 - - - -
253A ASP* 2.9 47.2 + - - +
830A SER 3.3 6.5 - - - +
831A VAL* 3.9 22.2 - - + -
855A ARG* 4.6 15.5 - - + -
856A THR* 1.3 73.6 - - - +
858A GLN* 1.3 70.2 + - - +
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Residues in contact with GLN 858 (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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135A PRO* 3.4 44.0 + - + +
136A ALA 5.6 0.5 - - - +
250A SER* 5.5 4.7 + - - -
251A THR 3.4 9.6 - - - +
252A GLY* 4.0 0.9 - - - -
256A THR* 3.5 27.3 - - + +
259A ILE* 4.3 8.3 - - - +
829A GLY* 3.5 2.9 - - - -
830A SER* 2.7 41.1 + - - +
832A GLU* 3.6 20.2 + - - +
853A ARG* 4.0 5.7 + - - +
856A THR* 3.9 16.7 + - + +
857A VAL* 1.3 86.5 - - - +
859A GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 859 (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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250A SER* 3.2 5.5 - - - -
251A THR* 2.8 35.4 + - - +
828A ARG 3.2 14.1 - - - -
829A GLY* 3.9 3.4 - - - -
858A GLN* 1.3 79.0 - - - +
860A GLY* 1.3 57.8 + - - -
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Residues in contact with GLY 860 (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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248A HIS* 4.9 5.2 - - - -
249A ALA 3.1 13.2 - - - -
250A SER* 3.8 7.2 - - - -
827A LEU* 3.2 8.0 - - - +
828A ARG* 3.0 36.9 + - - +
859A GLY* 1.3 73.9 - - - -
861A VAL* 1.3 66.3 + - - -
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Residues in contact with VAL 861 (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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247A LEU 4.0 0.3 - - - +
248A HIS* 3.4 6.5 - - - -
249A ALA* 2.9 33.5 + - + +
821A LEU* 6.4 1.6 - - + -
825A LEU* 4.4 15.0 - - + -
826A THR 3.9 5.4 - - - +
827A LEU* 4.2 16.6 - - + +
860A GLY* 1.3 79.3 - - - +
862A GLU* 1.3 70.6 + - - +
863A TYR* 5.8 0.7 - - + -
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Residues in contact with GLU 862 (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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132A ASP* 4.6 4.5 - - - +
246A LYS* 3.7 29.8 - - + +
247A LEU 3.3 9.6 - - - +
248A HIS* 4.1 12.2 - - + -
824A SER 3.3 3.3 - - - +
825A LEU* 3.5 4.3 - - - +
826A THR* 2.8 57.0 + - + +
828A ARG* 2.8 32.8 + - - +
861A VAL* 1.3 78.4 - - - +
863A TYR* 1.3 64.5 + - - +
864A ARG* 4.1 17.9 + - - +
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Residues in contact with TYR 863 (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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246A LYS* 3.3 2.4 - - - -
247A LEU* 2.8 55.3 + - + +
824A SER* 3.2 32.1 + - - -
825A LEU* 3.6 28.3 - - + -
861A VAL* 4.3 1.3 - - + -
862A GLU* 1.3 73.6 - - - +
864A ARG* 1.3 57.9 + - - +
865A PHE* 3.4 39.9 - + + +
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Residues in contact with ARG 864 (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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235A ASP 5.3 5.4 + - - -
236A PHE* 4.0 24.9 - - + -
241A LYS* 5.8 4.1 - - - +
245A GLY 3.4 15.0 - - - +
246A LYS* 4.1 7.2 - - + +
820A LYS* 5.7 8.7 - - - +
823A ASP 4.6 8.9 + - - +
824A SER* 2.9 37.8 + - - +
826A THR* 6.1 0.9 - - + -
862A GLU* 4.1 21.9 + - + +
863A TYR* 1.3 72.9 - - - +
865A PHE* 1.3 64.0 + - - +
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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