Contacts of the helix formed by residues 877 - 894 (chain A) in PDB entry 6CNC
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 877 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873A VAL* 3.9 6.3 + - + +
875A THR 3.5 0.2 - - - -
876A ALA* 1.3 77.4 - - + +
878A LYS* 1.3 53.7 + - - +
879A THR* 2.8 6.7 - - - -
880A ALA* 2.6 39.2 + - + +
481B ARG* 5.9 8.1 - - + +
482B LYS* 4.8 21.4 + - + +
487B ARG* 3.2 36.6 - - - +
506B GLU* 4.1 21.3 - - - +
22Y T 5.0 12.6 - - + +
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Residues in contact with LYS 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A ASP* 3.7 43.8 + - - +
875A THR 3.4 4.9 + - - +
876A ALA 3.4 1.0 - - - -
877A VAL* 1.3 77.9 - - - +
879A THR* 1.3 53.7 + - - +
880A ALA 3.0 1.0 + - - -
881A GLU* 3.4 11.3 + - + +
882A THR* 2.7 40.0 + - - +
1122A GLY* 6.3 0.6 - - - -
1123A VAL* 3.7 28.4 - - + +
1124A PRO* 5.4 4.9 - - - +
482B LYS* 5.0 17.9 - - - +
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Residues in contact with THR 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A THR* 3.9 10.1 + - + +
876A ALA* 2.4 26.6 + - - +
878A LYS* 1.3 76.3 - - - +
880A ALA* 1.3 58.8 + - - +
882A THR* 3.6 11.4 - - + +
883A GLY 2.9 19.2 + - - -
1100A PRO 6.2 2.7 - - - -
22Y T 2.8 45.0 + - - +
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Residues in contact with ALA 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A VAL* 2.6 27.7 + - + +
879A THR* 1.3 77.1 + - - +
881A GLU* 1.3 64.2 + - - +
884A TYR* 3.0 17.7 + - - +
481B ARG* 5.8 4.5 - - - +
482B LYS* 6.3 2.2 - - + -
21Y G 4.4 12.6 - - + +
22Y T 3.0 46.3 - - + +
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Residues in contact with GLU 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A LYS* 3.4 13.4 + - + +
880A ALA* 1.3 78.1 - - - +
882A THR* 1.3 63.1 + - - +
884A TYR* 3.4 9.9 - - + +
885A MET* 2.9 29.8 + - - +
1123A VAL* 3.7 31.3 - - - +
1127A LYS* 3.0 57.4 + - + +
482B LYS* 5.9 8.5 - - + +
21Y G 5.9 1.5 - - - +
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Residues in contact with THR 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A LYS* 2.7 29.6 + - - +
879A THR* 3.7 10.8 - - + +
880A ALA 3.0 0.4 - - - -
881A GLU* 1.3 82.3 + - - +
883A GLY* 1.3 60.0 + - - +
885A MET* 2.6 33.0 + - + +
886A SER* 2.9 13.2 + - - +
1098A GLY 4.0 11.9 - - - +
1100A PRO 3.4 35.8 + - - +
1123A VAL* 4.8 6.7 - - + +
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Residues in contact with GLY 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A THR 2.9 17.8 + - - -
882A THR* 1.3 73.8 - - - +
884A TYR* 1.3 62.1 + - - +
886A SER* 3.4 8.2 + - - -
887A ARG* 2.9 24.8 + - - +
1065B MET* 4.5 14.7 - - - +
22Y T 4.0 18.6 - - - -
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Residues in contact with TYR 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ALA 3.0 19.0 + - - +
881A GLU* 3.4 12.1 - - + +
883A GLY* 1.3 74.1 - - - +
885A MET* 1.3 63.8 + - - +
887A ARG* 3.2 25.2 + - - +
888A ARG* 2.9 76.0 + - + +
1127A LYS* 4.4 10.5 - - - -
1372A THR* 5.7 2.6 - - - -
1373A ARG 5.7 1.7 + - - -
1389A PHE* 5.2 4.9 - + - -
1390A GLU* 4.8 11.6 + - - -
20Y T 4.4 11.4 - - + +
21Y G 3.6 33.2 - - - -
22Y T 3.8 10.2 - - - -
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Residues in contact with MET 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A GLU* 2.9 21.7 + - - +
882A THR* 2.6 19.5 + - - +
884A TYR* 1.3 71.7 - - + +
886A SER* 1.3 58.9 + - - +
888A ARG* 3.4 19.1 - - - +
889A LEU* 2.9 38.6 + - + +
1097A ILE* 3.8 24.9 - - + +
1098A GLY* 4.4 16.4 - - - +
1123A VAL* 3.7 27.8 - - + +
1126A ILE* 3.5 34.5 - - + -
1127A LYS* 5.3 3.4 - - + -
1130A ILE* 4.1 9.2 - - + -
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Residues in contact with SER 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU 5.1 4.6 + - - -
882A THR* 2.9 11.7 + - - +
883A GLY* 3.9 6.2 - - - -
885A MET* 1.3 76.8 - - - +
887A ARG* 1.3 64.7 + - - +
889A LEU* 3.8 4.7 - - - +
890A MET* 2.9 24.3 + - - +
1094A ALA* 5.0 5.9 - - - +
1095A GLN* 5.3 11.0 + - - -
1098A GLY* 3.2 31.8 - - - -
1099A GLU* 4.2 0.9 + - - -
1065B MET* 4.3 20.8 - - - +
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Residues in contact with ARG 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ARG* 3.3 29.4 - - - +
883A GLY 2.9 17.0 + - - +
884A TYR* 3.5 19.9 - - - +
886A SER* 1.3 76.3 - - - +
888A ARG* 1.3 63.7 + - - +
890A MET* 3.1 18.3 - - + +
891A LYS* 2.9 24.5 + - + +
1388A SER 4.3 2.2 + - - -
1389A PHE* 3.2 45.3 + - - +
1390A GLU* 5.0 3.8 + - - -
1064B GLU* 2.5 51.1 + - + +
1065B MET* 4.8 13.1 - - + +
21Y G 4.2 12.5 + - - -
22Y T 5.7 1.1 - - - -
23Y G 4.7 12.1 - - - -
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Residues in contact with ARG 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A GLU* 5.0 1.0 + - - -
884A TYR* 2.9 59.3 + - + +
885A MET* 3.4 14.9 + - - +
887A ARG* 1.3 75.8 - - - +
889A LEU* 1.3 66.2 - - + +
891A LYS* 2.8 12.8 + - - +
892A SER* 3.1 14.2 + - - -
1127A LYS* 3.3 39.6 - - - +
1130A ILE* 5.7 1.2 - - - +
1131A ASN* 3.5 29.5 - - - +
1371A ILE* 3.6 35.3 + - + +
1372A THR* 4.6 6.7 - - - +
1376A LEU* 4.7 1.5 - - + +
1389A PHE* 3.5 34.3 - - + -
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Residues in contact with LEU 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A MET* 2.9 26.5 + - + +
886A SER* 3.8 4.7 - - - +
888A ARG* 1.3 79.6 - - + +
890A MET* 1.3 65.4 + - - +
892A SER* 3.6 1.0 + - - -
893A LEU* 3.0 28.6 + - + +
1094A ALA* 4.1 19.1 - - + +
1097A ILE* 4.1 39.3 - - + -
1098A GLY 4.9 2.0 - - - +
1130A ILE* 4.5 15.3 - - + -
1358A LEU* 4.0 22.7 - - + -
1371A ILE* 3.6 26.5 - - + -
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Residues in contact with MET 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A SER 2.9 14.4 + - - +
887A ARG* 3.1 22.2 - - + +
889A LEU* 1.3 73.8 - - - +
891A LYS* 1.3 83.1 + - + +
893A LEU 2.5 26.0 + - - -
894A GLU* 2.5 30.0 + - + +
1094A ALA* 3.8 16.7 - - + +
1095A GLN* 5.1 1.8 - - - +
1064B GLU* 3.9 24.0 - - + +
1065B MET* 5.3 1.6 - - - +
1067B ARG* 4.1 16.2 - - - +
1068B ASP* 3.1 46.2 - - - +
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Residues in contact with LYS 891 (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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369A SER* 5.2 3.0 + - - -
887A ARG* 2.9 19.1 + - + +
888A ARG 2.8 6.2 + - - +
890A MET* 1.3 94.1 - - + +
892A SER* 1.3 59.9 + - - +
894A GLU* 3.6 24.8 + - - +
1376A LEU* 3.3 13.5 - - + +
1380A ARG* 4.4 4.5 + - - -
1385A GLN* 4.4 15.8 - - - +
1388A SER* 3.7 24.4 + - - -
1389A PHE* 3.2 44.2 - - + -
1412A SER* 3.6 19.7 + - - -
1064B GLU* 3.8 19.1 + - - +
1067B ARG* 4.2 8.5 - - - +
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Residues in contact with SER 892 (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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888A ARG 3.1 5.0 + - - -
889A LEU 4.1 0.2 - - - -
890A MET 2.8 3.2 + - - -
891A LYS* 1.3 76.0 - - - +
893A LEU* 1.3 54.0 + - - +
894A GLU 3.3 1.8 - - - -
1361A VAL* 5.5 3.8 - - - +
1371A ILE* 3.6 27.4 + - - +
1376A LEU* 3.5 27.2 - - - +
1378A LYS* 3.0 30.3 + - - -
1380A ARG* 2.5 35.2 + - - +
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Residues in contact with LEU 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A LEU* 3.0 20.3 + - + +
890A MET* 2.5 8.6 + - - +
892A SER* 1.3 73.7 - - - +
894A GLU* 1.3 60.1 + - - -
895A ASP 3.4 4.7 + - - -
896A LEU* 3.9 9.5 + - + -
1090A GLY* 3.3 37.1 - - - +
1091A ALA* 5.4 0.2 - - - -
1093A GLY* 3.7 8.5 - - - -
1094A ALA* 3.4 21.8 - - + +
1097A ILE* 5.8 0.7 - - + -
1357A LEU* 3.6 17.5 - - + -
1358A LEU* 4.8 15.7 - - + -
1361A VAL* 3.6 41.1 - - + -
1380A ARG* 4.5 1.6 - - - +
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Residues in contact with GLU 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A MET* 2.5 35.1 + - + +
891A LYS* 3.6 25.6 + - - +
892A SER 3.3 2.2 - - - -
893A LEU* 1.3 73.5 - - - +
895A ASP* 1.3 59.7 + - - +
896A LEU 3.7 1.6 + - - -
1088A ALA* 5.4 0.5 - - - +
1091A ALA* 4.3 19.6 + - - +
1380A ARG* 4.7 0.4 - - - +
1385A GLN* 5.7 1.6 - - - +
1411A VAL* 3.6 18.8 - - + +
1412A SER* 3.2 30.0 + - - +
1423A ILE* 5.2 3.3 - - - +
1067B ARG* 2.9 38.7 + - - -
1068B ASP* 4.4 5.8 - - - +
1071B ILE* 4.5 8.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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