Contacts of the strand formed by residues 70 - 75 (chain 5) in PDB entry 6NRB
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 70 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843 THR* 3.5 36.1 - - - +
883 LEU* 3.5 33.0 - - + -
1233 MET* 3.7 11.4 - - + -
1243 CYS 3.2 4.7 - - - +
1253 LEU* 3.5 27.4 - - + +
1263 TRP* 3.4 2.6 - - - +
1443 LEU* 3.6 9.9 - - + -
665 LEU* 3.3 39.6 + - + -
675 THR* 2.7 25.2 - - + +
685 SER 3.1 2.6 + - - -
695 SER* 1.3 88.8 - - - +
715 TYR* 1.3 73.3 + - - +
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Residues in contact with TYR 71 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661 ARG* 5.4 1.3 - - + -
681 PHE* 4.5 10.8 - + - -
732 MET* 2.4 48.0 - - + +
782 LEU* 5.2 2.9 - - + -
1233 MET* 3.2 17.2 - - - +
1243 CYS* 2.3 44.5 + - + +
1263 TRP* 3.3 16.3 - + + -
1323 MET* 3.2 36.3 - - + -
635 LEU* 4.0 27.1 - - + -
645 VAL 3.7 5.2 - - - +
655 PRO* 3.4 28.3 - - + -
665 LEU* 3.4 9.6 - - - +
675 THR 5.1 1.3 - - - -
705 MET* 1.3 79.7 - - - +
725 VAL* 1.3 58.8 + - - +
735 PRO* 3.7 1.6 - - - +
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Residues in contact with VAL 72 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913 MET* 3.7 2.9 - - + -
993 ASN* 3.3 27.8 - - - +
1033 THR* 4.9 2.0 - - - +
1053 PHE* 5.4 0.7 - - + -
1173 VAL* 3.4 18.2 - - + -
1233 MET* 4.0 0.9 - - - -
734 ASP* 3.6 22.4 - - + +
744 VAL* 3.5 13.9 - - + -
635 LEU* 4.7 1.1 - - - -
645 VAL* 2.9 44.9 + - + +
665 LEU* 3.4 26.9 - - + +
715 TYR* 1.3 74.0 - - - +
735 PRO* 1.3 61.8 - - - +
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Residues in contact with PRO 73 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611 TYR* 5.3 2.2 - - - +
1053 PHE* 5.3 3.6 - - - -
1173 VAL* 3.0 24.7 - - - +
1193 PRO* 3.6 26.5 - - + +
1223 LYS* 3.8 26.0 - - + +
1233 MET* 3.9 19.1 - - - -
1243 CYS* 4.7 2.2 - - - +
615 GLU* 5.9 2.0 - - + -
625 LEU* 3.1 21.1 - - - +
635 LEU* 3.8 12.8 - - + -
715 TYR 3.7 8.1 - - - +
725 VAL* 1.3 89.4 - - + +
745 GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 74 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053 PHE* 4.4 4.9 - - - -
1163 SER 4.6 0.2 - - - -
1173 VAL* 2.9 18.6 - - - -
1183 PRO 4.5 0.9 - - - -
1193 PRO* 4.2 8.5 - - - +
615 GLU* 3.1 6.8 - - - +
625 LEU* 2.5 43.9 + - - +
735 PRO* 1.3 80.4 - - - +
755 LYS* 1.3 60.9 + - - -
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Residues in contact with LYS 75 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053 PHE* 3.4 9.1 - - - -
1153 ALA* 4.3 0.7 - - - +
1163 SER 3.3 20.6 + - - +
1173 VAL 4.1 0.6 + - - -
1183 PRO 4.6 11.9 + - - +
1193 PRO* 6.0 2.0 - - + -
595 GLY* 3.2 41.0 + - - +
605 LYS* 3.1 11.0 - - - +
615 GLU* 4.3 8.1 - - + +
745 GLY* 1.3 74.3 - - - -
765 LEU* 1.3 63.5 + - - +
775 HIS* 3.4 16.3 + - + -
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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