Contacts of the strand formed by residues 945 - 950 (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 HIS 945 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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941A PRO* 5.5 0.9 - - + -
942A PRO* 3.4 41.1 + - + +
943A GLY 3.7 2.6 + - - -
944A THR* 1.3 72.2 - - - +
946A LEU* 1.3 58.6 + - - +
956A ARG* 3.7 23.8 + - - +
958A PRO* 3.6 27.2 - - + +
985A PHE* 3.1 18.4 - - + -
989A ASP* 3.9 11.0 - - - +
1200A THR* 3.1 3.5 - - - +
1201A ALA 3.0 32.8 + - - +
1202A LEU* 3.7 28.3 - - + +
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Residues in contact with LEU 946 (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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944A THR 3.1 28.5 + - - +
945A HIS* 1.3 73.4 - - - +
947A LEU* 1.3 60.4 + - - +
948A PHE* 3.3 30.9 + - + -
956A ARG* 3.7 1.4 - - - +
957A LEU* 2.8 49.2 + - - +
959A LEU* 3.9 5.6 - - + +
985A PHE* 4.1 2.2 - - - -
1164A TYR* 3.6 45.8 - - + +
1187A PHE* 4.2 2.9 - - + -
1198A ILE* 3.6 19.3 - - + -
1199A THR 3.4 3.6 - - - -
1200A THR* 3.2 20.4 - - - +
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Residues in contact with LEU 947 (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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946A LEU* 1.3 73.2 - - - +
948A PHE* 1.3 60.6 + - - +
954A ILE* 3.8 17.5 - - + -
955A GLU 3.9 1.6 - - - -
956A ARG* 3.7 32.5 - - + +
973A LEU* 5.3 2.0 - - + -
983A LEU* 3.2 25.8 - - + +
984A ALA 3.4 25.1 - - - +
985A PHE* 3.8 19.4 - - + +
992A VAL* 3.6 29.8 - - + -
1198A ILE* 3.1 9.2 - - - +
1199A THR 2.9 35.8 + - - +
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Residues in contact with PHE 948 (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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946A LEU* 3.3 31.0 - - + -
947A LEU* 1.3 78.4 - - - +
949A ALA* 1.3 61.3 + - - +
954A ILE* 3.6 6.9 - - - +
955A GLU 2.8 36.3 + - - +
957A LEU* 3.6 20.4 - - + -
983A LEU* 3.6 5.4 - - - +
1171A ASN 5.6 0.2 - - - -
1173A VAL* 3.4 28.3 - - + -
1187A PHE* 3.3 39.9 - + + -
1188A GLN 5.4 0.4 - - - -
1190A HIS* 3.3 34.3 - + + -
1195A LEU* 3.9 14.6 - - + -
1197A GLY 3.6 4.0 - - - -
1198A ILE* 3.9 8.5 - - + -
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Residues in contact with ALA 949 (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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948A PHE* 1.3 77.0 - - - +
950A GLN* 1.3 63.3 + - - +
953A LYS 3.9 3.8 - - - -
954A ILE* 4.3 0.9 - - - -
980A ILE* 3.9 17.0 - - + -
981A ILE 5.1 0.7 - - - +
983A LEU* 3.4 36.8 - - + -
1195A LEU* 3.6 1.6 - - - +
1196A TYR* 3.0 30.6 + - + +
1197A GLY 3.0 16.9 + - - +
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Residues in contact with GLN 950 (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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949A ALA* 1.3 73.8 - - - +
951A THR* 1.3 66.3 + - - +
952A GLY 3.1 0.9 + - - -
953A LYS* 3.0 24.0 + - + +
980A ILE* 3.2 12.3 - - - +
1171A ASN* 2.7 45.0 + - - +
1190A HIS* 3.5 31.4 + - + +
1191A LYS 2.9 17.2 + - - -
1193A THR* 3.2 9.6 + - - +
1194A ARG* 3.1 17.5 - - - +
1195A LEU* 3.1 37.3 + - + +
1196A TYR* 4.6 0.2 - - - -
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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