Contacts of the helix formed by residues 995 - 1006 (chain K) in PDB entry 5ANC
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 VAL 995 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991K ALA* 4.4 1.8 - - + +
992K THR* 3.3 31.1 + - + +
994K ASP* 1.3 97.4 + - - +
996K LEU* 1.3 59.0 - - - +
997K GLY 3.6 0.4 - - - +
998K ARG* 4.3 8.7 - - + -
999K VAL* 3.1 23.8 + - + +
1044K THR* 3.9 24.2 - - + +
1047K LEU* 3.4 43.5 - - + +
1048K ALA* 3.9 7.7 - - + +
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Residues in contact with LEU 996 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991K ALA* 3.5 13.5 - - + -
992K THR 3.2 24.5 - - - +
993K GLY* 3.6 18.2 - - - +
994K ASP 3.5 1.2 - - - -
995K VAL* 1.3 77.3 - - - +
997K GLY* 1.3 62.6 + - - +
998K ARG 3.2 0.2 - - - -
999K VAL* 3.2 4.5 + - - +
1000K TYR* 2.9 29.0 + - - +
1013K GLU* 3.8 9.0 - - - +
1022K PHE* 4.0 15.7 - - + -
1024K ILE* 3.5 32.8 - - + +
1477N G 3.1 41.3 - - + +
1478N G 5.7 2.9 - - + +
1505N A 4.2 8.7 - - + +
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Residues in contact with GLY 997 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994K ASP 4.6 1.2 + - - -
995K VAL* 4.5 0.2 - - - +
996K LEU* 1.3 80.7 - - - +
998K ARG* 1.3 61.3 + - - +
1000K TYR* 3.2 9.8 + - - +
1001K ALA* 2.9 28.9 + - - +
1478N G 4.7 6.7 - - - -
1505N A 3.2 27.6 + - - +
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Residues in contact with ARG 998 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994K ASP 3.8 22.2 + - - +
995K VAL* 4.6 6.5 - - + +
996K LEU 3.2 0.4 - - - -
997K GLY* 1.3 77.6 - - - +
999K VAL* 1.3 64.4 + - + +
1001K ALA* 3.2 11.1 + - - +
1002K VAL* 3.2 25.7 + - - +
1043K ARG* 4.6 15.3 + - + +
1044K THR* 3.8 32.1 - - + +
1504N U 5.0 11.9 + - - -
1505N A 4.0 29.9 + - - -
1506N A 5.2 1.2 + - - -
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Residues in contact with VAL 999 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989K ILE* 3.9 34.3 - - + -
991K ALA* 5.1 1.3 - - + -
995K VAL* 3.1 22.0 - - + +
996K LEU* 3.2 11.1 + - - +
998K ARG* 1.3 81.1 - - + +
1000K TYR* 1.3 63.0 + - - +
1002K VAL* 3.2 7.3 + - - +
1003K LEU* 3.1 33.4 + - + +
1024K ILE* 4.7 7.6 - - + -
1036K PHE* 5.5 1.3 - - + -
1040K ILE* 4.0 17.2 - - + +
1048K ALA* 3.4 28.0 - - + -
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Residues in contact with TYR1000 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996K LEU 2.9 13.0 + - - +
997K GLY* 3.2 11.0 + - - +
999K VAL* 1.3 78.8 - - - +
1001K ALA* 1.3 57.0 + - - +
1003K LEU* 3.2 16.8 + - + +
1004K SER* 2.8 46.8 + - - -
1009K ARG* 5.1 5.1 - - - +
1010K VAL* 3.3 45.3 + - + +
1024K ILE* 6.4 0.7 - - + -
1476N U 4.0 13.9 + - - -
1478N G 3.5 17.0 - + - +
1479N A 3.3 41.3 + + - -
1483N C 4.9 10.8 + + - -
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Residues in contact with ALA1001 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997K GLY 2.9 12.9 + - - +
998K ARG* 3.3 15.0 - - - +
1000K TYR* 1.3 78.0 - - - +
1002K VAL* 1.3 57.6 + - - +
1004K SER* 3.2 9.8 + - - -
1005K LYS* 2.9 29.0 + - - +
1043K ARG* 4.5 16.5 + - - +
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Residues in contact with VAL1002 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998K ARG 3.2 14.2 + - - +
999K VAL* 3.2 8.7 + - - +
1001K ALA* 1.3 75.5 - - - +
1003K LEU* 1.3 64.2 + - - +
1005K LYS* 3.2 10.2 + - + +
1006K ARG* 3.0 36.5 + - - +
1036K PHE* 3.6 29.4 - - + -
1039K GLU* 4.4 15.7 - - + -
1040K ILE* 4.6 13.2 - - + -
1043K ARG* 3.8 36.8 - - + +
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Residues in contact with LEU1003 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987K CYS* 4.7 6.5 - - + -
989K ILE* 5.9 2.7 - - + -
999K VAL* 3.1 29.2 + - + +
1000K TYR* 3.4 26.7 - - + +
1002K VAL* 1.3 75.3 - - - +
1004K SER* 1.3 63.4 + - - +
1006K ARG 3.2 7.1 + - - -
1007K GLU 2.7 27.8 + - - +
1008K GLY 5.5 1.8 - - - -
1009K ARG* 5.7 5.2 - - - +
1010K VAL* 5.0 4.3 - - + +
1024K ILE* 5.8 2.7 - - + -
1026K ALA* 3.5 31.9 - - + -
1027K VAL 4.7 2.7 - - - +
1028K LEU* 3.7 39.3 - - + -
1036K PHE* 4.3 11.2 - - + -
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Residues in contact with SER1004 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000K TYR* 2.8 38.9 + - - -
1001K ALA* 3.2 10.9 + - - -
1003K LEU* 1.3 77.4 - - - +
1005K LYS* 1.3 63.9 - - - +
1006K ARG 3.4 0.2 + - - -
1007K GLU* 3.7 7.6 + - - -
1008K GLY 5.5 3.8 - - - -
1483N C 5.6 2.5 + - - -
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Residues in contact with LYS1005 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001K ALA 2.9 12.5 + - - +
1002K VAL* 3.2 11.9 + - + +
1004K SER* 1.3 78.2 - - - +
1006K ARG* 1.3 69.2 + - + +
1007K GLU 3.6 2.4 + - - -
1039K GLU* 5.8 4.0 - - + -
1043K ARG* 4.5 22.4 - - - +
3175N C 3.3 53.5 + - + +
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Residues in contact with ARG1006 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002K VAL* 3.0 31.0 + - - +
1003K LEU 3.2 0.6 + - - -
1005K LYS* 1.3 95.6 - - + +
1007K GLU* 1.3 72.6 + - - +
1028K LEU* 3.1 17.0 - - + +
1029K PRO* 3.7 4.5 - - - +
1031K ALA 5.3 0.4 + - - -
1032K GLU* 3.1 61.2 + - + +
1034K PHE 3.3 14.3 + - - -
1035K GLY* 3.6 20.0 + - - -
1036K PHE* 3.8 16.6 - - - +
1039K GLU* 4.1 15.4 + - - +
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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