Contacts of the strand formed by residues 991 - 996 (chain A) in PDB entry 1NDX
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 991 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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985A PHE* 3.2 2.7 - - - +
986A ASP* 2.9 19.1 + - - +
990A LYS* 1.3 91.4 - - + +
992A VAL* 1.3 62.7 + - - +
993A TYR* 3.1 36.1 - - + +
1004A ARG* 3.7 40.2 - - + -
1005A ALA 3.5 5.4 - - - +
1006A SER* 4.2 22.7 - - - +
1007A LEU* 4.2 0.4 - - - +
1013A THR* 3.7 14.6 - - + +
1031A LEU* 4.2 18.8 - - + -
1032A GLY* 5.3 0.4 - - - -
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Residues in contact with VAL 992 (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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947A LEU* 3.6 21.3 - - + -
954A ILE* 4.8 0.7 - - + -
973A LEU* 3.9 18.4 - - + -
985A PHE* 3.5 25.8 - - + -
991A MET* 1.3 74.4 - - - +
993A TYR* 1.3 63.6 + - - +
994A TRP* 4.4 11.4 - - + -
1003A GLY 3.3 0.4 - - - +
1004A ARG* 3.2 6.6 - - - -
1005A ALA* 2.8 58.1 + - + +
1007A LEU* 3.6 29.6 - - + -
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Residues in contact with TYR 993 (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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983A LEU* 3.2 6.3 - - - +
984A ALA 2.8 34.5 + - - +
985A PHE* 3.8 3.8 - - - -
986A ASP* 3.5 24.2 - - + +
991A MET* 3.1 34.6 - - + +
992A VAL* 1.3 77.7 - - - +
994A TRP* 1.3 62.0 + - - +
1002A ILE* 3.6 17.7 - - + -
1003A GLY 3.4 2.9 - - - -
1004A ARG* 3.2 40.8 + - + -
1026A ILE* 3.1 23.1 - - + +
1028A VAL* 3.4 22.0 - - + +
1031A LEU 2.9 26.5 + - - -
1035A ILE* 3.9 12.8 - - + -
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Residues in contact with TRP 994 (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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954A ILE* 3.8 35.2 - - + +
973A LEU* 5.9 1.0 - - - +
975A VAL* 3.7 33.4 - - + +
976A PRO* 4.7 9.9 - - + -
977A ALA* 3.6 16.6 - - + -
980A ILE* 3.9 9.6 - - + -
982A GLY 4.0 2.7 - - - -
983A LEU* 3.8 4.5 - - + -
992A VAL* 4.4 12.8 - - + +
993A TYR* 1.3 76.3 - - - +
995A THR* 1.3 63.2 + - - +
996A ASP* 3.2 31.4 - - - -
1001A SER 3.6 0.7 - - - +
1002A ILE* 3.3 2.6 - - - +
1003A GLY* 2.8 60.8 + - - -
1005A ALA* 4.3 11.9 - - - +
1012A PRO* 4.9 17.7 - - + -
1015A ILE* 6.6 0.4 - - + -
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Residues in contact with THR 995 (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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980A ILE* 3.9 2.6 - - - +
981A ILE* 2.8 49.7 + - - +
982A GLY* 2.9 17.1 + - - +
994A TRP* 1.3 73.7 - - - +
996A ASP* 1.3 66.2 + - - +
1001A SER 3.4 3.6 - - - -
1002A ILE* 3.5 13.5 - - + -
1023A PRO* 2.9 47.2 + - + -
1024A GLU 4.5 1.1 - - - +
1025A GLY 4.8 0.9 - - - +
1026A ILE* 3.4 23.1 - - + -
1037A TRP* 4.5 0.7 - - + -
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Residues in contact with ASP 996 (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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977A ALA* 3.1 25.5 - - + +
979A VAL 4.4 6.7 - - - +
980A ILE* 5.1 0.9 - - - -
981A ILE* 4.2 0.4 - - - -
994A TRP* 3.2 24.8 - - - -
995A THR* 1.3 78.0 - - - +
997A ILE* 1.3 68.6 + - - +
999A GLU* 2.9 56.7 - - + +
1001A SER* 3.0 28.0 + - - +
1023A PRO* 3.2 12.0 - - - +
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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