Contacts of the strand formed by residues 822 - 830 (chain B) in PDB entry 5NC5
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 LEU 822 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ALA 5.8 3.4 - - - +
161A ASN* 5.9 8.1 - - - +
685B ILE* 3.7 29.1 - - + +
686B ASP 3.7 13.9 - - - +
687B GLN* 4.2 23.8 - - - +
818B ARG* 3.1 4.7 - - - -
819B TYR 2.8 31.5 + - - +
820B ASN* 4.2 12.1 - - + +
821B GLY* 1.3 84.6 - - - +
823B PRO* 1.3 72.4 - - + +
824B SER* 4.0 0.2 - - - -
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Residues in contact with PRO 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766A GLY 5.4 4.9 - - - +
58B GLN* 4.8 5.6 - - - +
685B ILE* 3.6 1.6 - - - +
686B ASP* 2.9 57.2 + - + +
689B GLY* 6.4 0.4 - - - -
691B GLY 6.5 0.7 - - - -
695B LEU* 4.0 8.9 - - + +
816B LEU* 6.4 1.6 - - + -
817B GLU 3.4 11.0 - - - +
818B ARG* 3.6 24.2 - - + +
822B LEU* 1.3 89.8 - - + +
824B SER* 1.3 60.1 - - - +
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Residues in contact with SER 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B GLU* 3.0 19.5 + - - -
684B LEU 3.1 13.7 - - - -
685B ILE* 4.3 4.7 - - - -
695B LEU* 3.9 3.9 - - - +
817B GLU* 3.0 32.4 + - - +
818B ARG 3.5 15.1 + - - -
819B TYR* 3.6 25.0 - - - +
822B LEU 3.4 0.6 + - - -
823B PRO* 1.3 77.4 - - - +
825B MET* 1.3 70.3 + - - +
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Residues in contact with MET 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683B GLU* 3.5 2.7 - - - -
684B LEU* 3.0 39.2 + - + +
692B HIS* 3.4 26.7 - - + +
695B LEU* 3.6 19.5 - - + -
696B THR* 3.1 42.8 - - + +
699B ARG* 3.8 42.0 - - + +
817B GLU* 3.2 7.2 - - - +
824B SER* 1.3 80.1 - - - +
826B GLU* 1.3 63.0 - - - +
827B ILE* 3.8 2.3 + - - +
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Residues in contact with GLU 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681B ASP* 2.5 37.0 - - - +
682B PHE 3.5 3.8 - - - +
683B GLU* 3.4 28.3 + - - +
699B ARG* 5.5 0.3 - - - -
718B PRO* 3.6 4.0 - - - +
719B ASN* 3.0 58.4 + - + +
720B GLY 4.6 0.7 + - - -
817B GLU* 2.9 19.1 + - - +
825B MET* 1.3 74.2 - - - +
827B ILE* 1.3 67.7 + - - +
828B LEU* 4.1 2.2 - - + +
860B THR* 4.5 1.6 - - - +
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Residues in contact with ILE 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B PHE* 4.4 1.2 - - + +
681B ASP* 3.7 0.7 - - - +
682B PHE* 2.7 68.6 + - + +
684B LEU* 4.4 11.7 - - + -
699B ARG* 4.1 26.7 - - + +
702B LEU* 3.9 20.2 - - + -
703B LEU* 4.4 9.6 - - + -
716B VAL* 4.0 19.5 - - + -
717B ARG 3.5 13.7 - - - +
718B PRO* 4.8 3.6 - - + -
825B MET 4.3 2.0 - - - +
826B GLU* 1.3 79.2 - - - +
828B LEU* 1.3 73.3 + - - +
844B MET* 4.6 8.5 - - + -
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Residues in contact with LEU 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B PHE* 3.9 15.5 - - - +
681B ASP* 3.3 29.4 - - - +
715B SER 4.0 1.6 - - - -
716B VAL* 3.3 2.8 - - - +
717B ARG* 2.8 67.7 + - - +
719B ASN* 3.4 40.4 - - + +
826B GLU* 4.1 6.7 - - - +
827B ILE* 1.3 77.9 - - - +
829B GLY* 1.3 58.9 + - - +
862B MET* 4.9 5.8 - - + -
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Residues in contact with GLY 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B GLY* 3.3 4.3 - - - -
680B PHE* 2.9 45.5 + - - +
714B THR 3.9 2.0 - - - -
715B SER 3.6 14.4 - - - -
716B VAL* 4.0 2.7 - - - -
717B ARG* 4.0 4.1 - - - +
828B LEU* 1.3 77.7 - - - +
830B GLN* 1.3 65.0 + - - -
862B MET* 5.3 0.2 - - - +
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Residues in contact with GLN 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B THR* 5.2 9.3 + - - +
678B THR* 3.3 39.5 - - + +
679B GLY* 4.0 0.9 - - - -
680B PHE* 3.7 12.0 - - - -
713B LEU* 3.7 5.2 - - - -
714B THR* 3.0 50.1 + - + +
715B SER* 4.0 19.6 + - - -
717B ARG* 4.6 7.1 - - - +
829B GLY* 1.3 75.9 + - - +
831B ALA* 1.3 62.8 + - - +
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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