Contacts of the strand formed by residues 953 - 958 (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 LYS 953 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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949A ALA* 3.9 0.7 - - - -
950A GLN 3.0 24.8 + - - +
951A THR 3.4 1.6 - - - -
952A GLY* 1.3 76.9 - - - +
954A ILE* 1.3 65.2 + - - +
955A GLU* 4.1 11.4 - - + +
972A PHE* 3.8 27.1 - - + -
973A LEU 3.7 26.0 - - - +
974A HIS* 3.6 34.4 - - - +
980A ILE* 4.1 0.4 - - - -
1190A HIS* 3.0 38.3 + - + +
1191A LYS* 3.6 34.4 - - + +
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Residues in contact with ILE 954 (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* 3.8 18.8 - - + -
948A PHE 3.6 1.6 - - - -
949A ALA* 4.1 2.7 - - + -
953A LYS* 1.3 74.2 - - - +
955A GLU* 1.3 61.7 + - - +
956A ARG 4.1 0.3 + - - -
971A ALA 3.5 1.7 - - - +
972A PHE* 3.8 0.5 - - - -
973A LEU* 2.8 64.3 + - + +
975A VAL* 3.8 19.7 - - + -
980A ILE* 3.5 33.7 - - + -
983A LEU* 3.4 36.3 - - + -
992A VAL* 4.8 0.9 - - + -
994A TRP* 3.8 15.0 - - + -
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Residues in contact with GLU 955 (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* 3.9 1.8 - - - -
948A PHE 2.8 35.0 + - - -
953A LYS* 3.8 5.9 + - + +
954A ILE* 1.3 74.4 - - - +
956A ARG* 1.3 58.6 + - - +
957A LEU* 3.1 42.8 - - + +
969A ALA* 3.5 11.4 - - + +
971A ALA 3.1 12.3 - - - +
972A PHE* 3.5 28.1 - - + -
1189A PRO 5.0 3.3 - - - +
1190A HIS* 3.4 44.6 + - + +
1191A LYS* 4.3 2.8 + - - +
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Residues in contact with ARG 956 (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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945A HIS* 3.7 32.1 + - - -
946A LEU 3.7 8.1 - - - +
947A LEU* 3.7 14.6 - - + +
954A ILE 4.1 0.2 + - - -
955A GLU* 1.3 70.3 - - - +
957A LEU* 1.3 60.9 + - - +
958A PRO* 4.1 6.4 - - + +
969A ALA* 3.4 3.8 - - - -
970A LYS* 2.8 40.1 + - + +
971A ALA* 3.0 30.6 + - + +
985A PHE* 3.7 27.7 - - + -
989A ASP* 3.3 23.0 + - - -
1007A LEU* 4.2 26.7 + - + +
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Residues in contact with LEU 957 (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* 2.8 38.4 + - - +
948A PHE* 3.6 30.3 - - + -
955A GLU* 3.1 53.6 - - + +
956A ARG* 1.3 76.7 - - - +
958A PRO* 1.3 64.8 - - - +
967A THR 5.3 0.2 - - - +
968A GLU* 3.1 3.6 - - - +
969A ALA* 3.6 20.0 - - + +
1187A PHE* 3.3 37.3 - - + -
1188A GLN 5.9 1.8 - - - +
1190A HIS* 6.1 0.2 - - + -
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Residues in contact with PRO 958 (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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941A PRO* 3.7 29.1 - - + +
944A THR 3.2 10.1 - - - +
945A HIS* 3.6 32.3 - - + +
946A LEU 4.5 0.4 - - - -
956A ARG* 4.0 7.4 - - + +
957A LEU* 1.3 83.3 - - - +
959A LEU* 1.3 64.9 + - - +
966A LYS* 4.4 0.5 - - - +
967A THR 3.4 1.7 + - - -
968A GLU 3.0 33.8 + - - +
970A LYS* 3.6 30.3 - - + -
1187A PHE* 4.2 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