Contacts of the strand formed by residues 995 - 1005 (chain A) in PDB entry 1K3A
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 GLU 995 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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990A GLY* 4.1 8.5 + - - -
992A VAL* 3.1 38.5 + - + +
993A LYS 2.8 5.8 + - - +
994A ASP* 1.3 80.3 - - - +
996A PRO* 1.3 72.2 - - + +
997A GLU* 3.3 17.1 + - - +
998A THR* 2.5 37.1 + - - +
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Residues in contact with PRO 996 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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989A LYS* 3.4 8.1 - - - +
990A GLY* 2.8 25.7 + - - -
994A ASP 4.0 5.6 - - - +
995A GLU* 1.3 85.1 - - + +
997A GLU* 1.3 65.3 + - + +
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Residues in contact with GLU 997 (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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987A VAL* 3.6 24.8 - - + +
988A ALA 3.2 10.8 - - - +
989A LYS* 4.0 22.7 + - + -
990A GLY 4.6 0.2 - - - +
995A GLU* 3.3 15.2 - - - +
996A PRO* 1.3 84.1 - - + +
998A THR* 1.3 66.6 + - - +
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Residues in contact with THR 998 (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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987A VAL* 3.3 6.1 - - - -
988A ALA 2.7 32.8 + - - -
991A VAL* 3.7 17.3 - - - +
992A VAL* 3.6 23.2 + - + +
995A GLU* 2.5 31.8 + - - +
997A GLU* 1.3 76.7 - - - +
999A ARG* 1.3 76.5 + - - +
1000A VAL* 3.5 7.1 - - + +
1036A LEU* 4.5 7.0 - - + -
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Residues in contact with ARG 999 (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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985A GLU* 2.9 28.9 + - - -
986A GLY 3.5 9.2 - - - +
987A VAL* 4.5 9.6 - - + +
998A THR* 1.3 83.0 - - - +
1000A VAL* 1.3 64.3 + - - +
1036A LEU* 4.9 0.9 - - - +
1050A GLU* 5.1 0.2 - - - -
1051A LEU* 3.6 38.3 + - + +
1053A THR* 4.2 17.2 - - - +
1115A GLU* 5.9 0.2 + - - -
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Residues in contact with VAL1000 (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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969A ILE* 5.3 0.2 - - + -
985A GLU* 3.5 7.4 - - - +
986A GLY 2.9 44.3 + - - +
987A VAL 3.9 10.8 - - - +
988A ALA* 4.0 17.7 - - + +
991A VAL* 4.8 0.4 - - + -
998A THR* 3.5 13.2 - - + +
999A ARG* 1.3 82.2 - - - +
1001A ALA* 1.3 61.2 + - - +
1002A ILE* 3.9 18.6 - - + -
1036A LEU* 3.8 22.9 - - + -
1048A ILE* 4.5 11.7 - - + -
1049A MET 3.5 8.3 - - - +
1051A LEU* 4.0 8.7 - - - +
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Residues in contact with ALA1001 (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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300A ACP 3.4 50.7 - - + +
975A LEU* 4.5 2.0 - - + -
983A VAL* 4.8 2.5 - - + -
984A TYR 3.4 6.3 - - - +
985A GLU* 4.7 0.2 - - - +
1000A VAL* 1.3 75.2 - - - +
1002A ILE* 1.3 60.3 + - - +
1003A LYS* 4.0 3.1 - - + +
1047A VAL 3.8 1.0 - - - +
1048A ILE* 3.4 4.7 - - - -
1049A MET* 2.9 38.0 + - + +
1050A GLU 4.1 0.9 - - - +
1051A LEU* 4.2 4.6 - - + +
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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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969A ILE* 3.5 18.2 - - + -
970A THR 3.6 12.3 - - - +
971A MET* 3.5 30.7 - - + -
982A MET 3.8 1.7 - - - +
983A VAL* 3.3 3.7 - - - +
984A TYR* 2.5 44.3 + - + +
985A GLU 4.5 0.9 - - - -
986A GLY* 4.0 12.8 - - - +
1000A VAL* 3.9 14.6 - - + +
1001A ALA* 1.3 77.6 - - - +
1003A LYS* 1.3 62.6 + - - +
1004A THR* 4.2 3.4 - - + -
1046A LEU* 3.9 39.7 - - + -
1047A VAL 3.7 4.0 - - - +
1048A ILE* 4.2 8.5 - - + -
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Residues in contact with LYS1003 (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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300A ACP 3.8 43.0 + - - +
978A GLY* 5.8 0.7 - - - -
979A SER* 5.7 2.5 - - - +
980A PHE* 5.8 6.1 - - - -
982A MET 4.3 2.5 - - - -
983A VAL* 4.2 23.1 - - + +
1001A ALA* 5.0 3.8 - - + +
1002A ILE* 1.3 75.0 - - - +
1004A THR* 1.3 60.4 + - - +
1017A PHE* 3.5 23.3 - - + -
1020A GLU* 4.8 13.7 + - - -
1046A LEU* 3.4 4.3 - - - -
1047A VAL* 2.9 41.0 + - + +
1049A MET* 3.9 26.9 - - + -
1122A GLY 5.9 1.2 + - - -
1123A ASP* 4.6 9.9 + - - -
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Residues in contact with THR1004 (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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971A MET* 4.8 0.2 - - - -
980A PHE 3.6 1.2 - - - -
981A GLY* 3.3 22.4 + - - +
982A MET* 2.8 34.1 + - - +
984A TYR* 3.6 27.3 - - + -
1002A ILE* 4.0 2.5 - - + +
1003A LYS* 1.3 76.2 - - - +
1005A VAL* 1.3 67.1 + - - +
1006A ASN* 4.9 0.5 + - - -
1017A PHE* 4.0 5.5 - - - -
1044A PRO* 4.4 11.0 - - + -
1045A THR 3.4 5.8 - - - -
1046A LEU* 3.1 29.4 - - + -
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Residues in contact with VAL1005 (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 PHE* 3.6 13.2 - - + +
1004A THR* 1.3 76.2 - - - +
1006A ASN* 1.3 71.2 + - - +
1007A GLU* 3.2 2.9 + - - -
1009A ALA* 3.5 25.6 - - + -
1013A GLU 5.3 0.2 - - - -
1014A ARG* 3.8 22.0 - - + +
1017A PHE* 3.1 53.2 - - + -
1043A GLN* 4.9 0.5 - - - +
1044A PRO* 3.7 17.7 - - - +
1045A THR* 3.1 22.0 + - + +
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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