Contacts of the strand formed by residues 1001 - 1006 (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 SER1001 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994A TRP 3.6 0.3 - - - +
995A THR* 3.4 3.3 - - - -
996A ASP* 3.0 43.5 + - - +
999A GLU* 2.7 19.8 + - - +
1000A PRO* 1.3 75.1 - - - +
1002A ILE* 1.3 63.2 + - - +
1003A GLY 5.1 0.2 + - - -
1015A ILE* 4.0 20.2 - - - +
1016A ILE 3.0 19.3 - - - -
1017A ARG* 3.9 8.1 - - - -
1023A PRO* 3.8 1.4 - - - +
1037A TRP* 3.9 2.5 - - - -
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Residues in contact with ILE1002 (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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993A TYR* 3.6 39.7 - - + -
994A TRP 3.3 8.5 - - - +
995A THR* 3.5 12.3 - - + -
1001A SER* 1.3 74.2 - - - +
1003A GLY* 1.3 61.7 + - - +
1004A ARG 3.3 0.2 + - - -
1014A THR 3.2 5.4 - - - +
1015A ILE* 3.7 1.2 - - - -
1016A ILE* 2.9 43.7 + - + +
1026A ILE* 3.8 19.1 - - + -
1035A ILE* 3.6 23.1 - - + -
1037A TRP* 3.4 42.8 - - + -
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Residues in contact with GLY1003 (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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992A VAL 3.3 5.7 - - - +
993A TYR* 3.4 0.2 - - - -
994A TRP* 2.8 74.0 + - - -
1001A SER* 4.0 1.2 + - - -
1002A ILE* 1.3 70.1 - - - +
1004A ARG* 1.3 61.3 + - - -
1005A ALA 3.7 0.2 - - - -
1012A PRO* 5.6 2.9 - - - -
1014A THR 3.9 2.9 - - - -
1015A ILE* 5.0 6.7 - - - -
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Residues in contact with ARG1004 (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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991A MET* 3.7 37.6 - - + -
992A VAL 3.2 6.1 - - - -
993A TYR* 3.2 33.7 + - + -
1002A ILE 3.3 1.4 + - - -
1003A GLY* 1.3 70.0 - - - +
1005A ALA* 1.3 59.8 + - - +
1012A PRO* 3.3 3.4 - - - +
1013A THR* 2.8 26.8 + - - +
1014A THR* 2.9 42.1 + - - +
1016A ILE* 4.0 9.0 - - + +
1031A LEU 3.4 17.7 + - - -
1032A GLY* 3.5 21.1 - - - -
1035A ILE* 4.1 7.9 - - - +
1050A LEU* 3.4 37.4 + - - +
1051A ASP* 5.1 1.4 + - - -
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Residues in contact with ALA1005 (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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973A LEU* 4.9 7.2 - - + -
975A VAL* 6.4 0.4 - - + -
991A MET* 4.4 2.7 - - - -
992A VAL* 2.8 53.2 + - + +
994A TRP* 4.3 12.1 - - + +
1003A GLY 3.5 0.6 + - - -
1004A ARG* 1.3 74.0 - - - +
1006A SER* 1.3 67.9 + - - +
1010A GLY 4.9 2.5 - - - -
1011A GLU 3.2 13.0 - - - +
1012A PRO* 3.8 14.1 - - + -
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Residues in contact with SER1006 (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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973A LEU* 5.6 1.0 - - - +
990A LYS 3.6 10.3 + - - -
991A MET* 4.2 19.0 - - - +
992A VAL* 5.4 0.3 - - - +
1004A ARG 4.2 0.4 + - - -
1005A ALA* 1.3 74.5 - - - +
1007A LEU* 1.3 63.3 + - - +
1008A HIS* 3.0 24.9 + - - +
1009A GLY 3.0 22.8 - - - +
1010A GLY* 3.1 13.9 - - - -
1011A GLU* 2.9 13.8 + - - -
1013A THR* 4.4 8.7 - - - -
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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