Contacts of the helix formed by residues 979 - 996 (chain A) in PDB entry 6CIM
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 SER 979 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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977A ARG* 3.0 4.9 + - - -
978A GLN* 1.3 79.7 - - - +
980A LYS* 1.3 59.1 + - - +
981A CYS* 3.4 22.5 - - - -
982A TYR* 2.9 20.5 + - - -
983A GLU* 2.7 36.3 + - - +
37G C 3.7 30.6 + - - -
38G T 4.2 7.5 + - - -
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Residues in contact with LYS 980 (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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553A ILE* 3.3 43.5 - - + +
617A GLU* 3.2 25.7 + - - -
659A LEU* 4.1 12.2 - - - +
972A ARG* 4.4 3.0 - - - +
979A SER* 1.3 72.5 + - - +
981A CYS* 1.3 62.9 + - - +
983A GLU* 3.4 29.2 - - - +
984A MET* 4.0 2.3 + - - +
38G T 4.5 16.6 + - - +
39G G 4.8 13.9 - - - +
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Residues in contact with CYS 981 (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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553A ILE* 4.4 13.0 - - + +
555A LYS* 4.1 20.3 - - - +
979A SER* 3.4 14.8 - - - -
980A LYS* 1.3 81.6 - - - +
982A TYR* 1.3 93.0 + - + +
984A MET* 4.0 2.1 + - - +
985A GLU* 4.0 15.9 + - - +
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Residues in contact with TYR 982 (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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977A ARG* 3.0 51.6 - - + +
979A SER* 2.9 25.3 + - - +
981A CYS* 1.3 92.2 - - + +
983A GLU* 1.3 65.1 + - - +
984A MET 3.1 2.7 - - - -
985A GLU* 3.2 21.2 + - - +
986A ASP* 2.9 25.6 + - - -
36G A 6.3 1.1 - - - -
37G C 5.2 11.4 - - - -
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Residues in contact with GLU 983 (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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659A LEU* 4.9 3.1 - - - +
972A ARG* 3.1 45.3 + - + +
976A ALA* 4.1 12.1 - - + +
977A ARG 3.1 22.8 + - - +
978A GLN* 3.5 18.6 + - - +
979A SER 2.7 17.5 + - - +
980A LYS* 3.4 37.9 + - - +
982A TYR* 1.3 71.6 - - - +
984A MET* 1.3 69.6 + - + +
986A ASP* 3.3 2.5 + - - +
987A VAL* 2.9 34.7 + - - +
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Residues in contact with MET 984 (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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553A ILE* 3.8 33.0 - - + +
554A ALA* 4.8 0.4 - - - +
555A LYS* 4.0 19.7 - - + +
657A LEU* 3.5 42.9 - - + +
658A MET* 3.7 16.6 - - - +
659A LEU* 4.0 14.6 - - + +
968A PHE* 3.8 31.0 - - + -
972A ARG* 6.1 1.1 - - - -
980A LYS 4.0 3.5 + - - +
981A CYS 4.2 1.8 - - - +
982A TYR 3.1 0.4 - - - -
983A GLU* 1.3 89.3 - - + +
985A GLU* 1.3 58.3 + - - +
987A VAL* 3.2 7.0 + - - +
988A LEU* 2.9 26.5 + - - +
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Residues in contact with GLU 985 (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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534A ILE* 3.4 45.1 - - + +
555A LYS* 4.1 16.6 - - + +
977A ARG* 4.4 6.5 + - - -
981A CYS 4.0 5.7 + - - +
982A TYR* 3.3 38.9 - - - +
984A MET* 1.3 79.6 - - - +
986A ASP* 1.3 62.9 + - - +
988A LEU* 4.1 4.0 - - - -
989A LYS* 2.9 26.5 + - - +
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Residues in contact with ASP 986 (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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975A ASN 3.8 15.9 - - - +
976A ALA* 3.9 4.7 - - - -
977A ARG* 2.9 58.8 + - - +
982A TYR 2.9 18.3 + - - +
983A GLU 3.7 3.8 - - - +
985A GLU* 1.3 80.0 - - - +
987A VAL* 1.3 65.3 + - - +
989A LYS* 4.1 7.1 + - - +
990A HIS* 2.9 35.3 + - + -
23J G 3.7 12.5 - - - +
24J A 4.8 2.4 + - - -
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Residues in contact with VAL 987 (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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657A LEU* 3.7 6.1 - - + -
968A PHE* 3.6 40.4 - - + +
971A PHE* 4.1 25.0 - - + +
972A ARG* 3.9 36.8 - - + +
976A ALA* 4.3 2.0 - - + -
983A GLU 2.9 23.8 + - - +
984A MET* 3.6 7.2 - - - +
986A ASP* 1.3 77.1 - - - +
988A LEU* 1.3 61.4 + - - +
990A HIS* 3.9 0.7 - - - +
991A HIS* 2.9 24.1 + - - +
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Residues in contact with LEU 988 (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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534A ILE* 3.9 15.5 - - + -
555A LYS* 4.2 5.8 - - + -
556A ARG* 4.1 25.4 - - - +
557A PHE* 3.8 29.8 - - + -
654A PRO* 4.1 26.5 - - + +
655A LEU 4.7 4.0 - - - -
657A LEU* 3.8 34.7 - - + +
984A MET 2.9 16.5 + - - +
985A GLU* 3.6 5.6 - - - +
986A ASP 3.2 0.2 - - - -
987A VAL* 1.3 77.1 - - - +
989A LYS* 1.3 56.1 + - - +
991A HIS* 3.1 3.3 + - - +
992A TRP* 2.9 28.2 + - - +
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Residues in contact with LYS 989 (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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471A ARG* 4.4 0.8 - - - +
507A GLU* 2.9 41.9 + - - -
511A LEU* 4.0 29.6 - - + -
534A ILE* 4.2 13.0 - - + +
557A PHE* 5.0 1.3 - - - -
985A GLU 2.9 17.6 + - - +
986A ASP* 4.2 7.5 + - - +
988A LEU* 1.3 76.0 - - - +
990A HIS* 1.3 87.0 + - + +
992A TRP* 3.3 8.1 + - - +
993A LEU* 3.0 35.1 + - + +
23J G 4.5 3.6 + - - -
24J A 3.7 25.2 + - - +
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Residues in contact with HIS 990 (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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471A ARG* 3.6 31.1 + - - -
472A VAL* 4.5 12.8 - - - +
971A PHE* 3.8 26.1 - + + -
975A ASN* 3.1 51.9 + - + +
986A ASP* 2.9 30.0 + - - +
987A VAL* 4.1 2.2 - - - +
989A LYS* 1.3 95.6 + - - +
991A HIS* 1.3 56.6 + - - +
993A LEU* 3.8 5.7 - - - +
994A TYR* 2.9 29.6 + - - +
23J G 4.0 11.3 + - - -
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Residues in contact with HIS 991 (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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602A MET* 4.9 18.4 - - + -
621A ARG* 5.2 6.4 - - - -
649A GLU* 5.0 3.4 + - - +
652A CYS 4.7 5.3 + - - -
654A PRO* 3.7 30.5 - - + +
657A LEU* 4.6 10.8 - - + +
964A GLY* 5.0 3.6 - - - -
967A LEU* 4.1 29.3 - - + +
968A PHE* 5.0 4.6 + - - -
971A PHE* 4.0 19.7 - + + -
987A VAL* 2.9 22.6 + - - +
988A LEU* 3.6 4.5 - - - +
990A HIS* 1.3 72.6 - - - +
992A TRP* 1.3 68.1 + - - +
994A TYR* 3.2 7.3 + + - +
995A THR* 3.1 33.4 + - + +
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Residues in contact with TRP 992 (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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510A LEU* 2.8 29.5 + - + -
511A LEU* 3.5 20.9 - - + -
512A PRO* 3.7 5.7 - - + +
557A PHE* 3.5 23.6 - + + -
562A ALA* 3.5 27.1 - - + -
565A SER* 3.4 26.8 + - - -
566A ALA 3.9 4.3 - - - -
569A ASP* 6.2 1.2 - - + +
624A PHE* 4.2 3.6 - + - -
653A LYS* 3.3 48.7 - - + +
654A PRO* 3.5 29.2 - - + +
988A LEU 2.9 12.9 + - - +
989A LYS 3.4 8.3 - - - +
991A HIS* 1.3 74.9 - - - +
993A LEU* 1.3 65.8 + - - +
995A THR* 2.6 23.3 + - - -
996A SER* 3.3 8.1 + - - -
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Residues in contact with LEU 993 (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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468A LEU* 4.2 14.4 - - + -
471A ARG* 5.1 0.9 - - - +
472A VAL* 4.0 26.3 - - + +
507A GLU* 3.6 34.1 - - + +
510A LEU* 3.9 30.3 - - + -
511A LEU* 4.3 13.7 - - + -
989A LYS* 3.0 35.8 + - + +
990A HIS* 3.8 6.3 - - - +
992A TRP* 1.3 77.5 - - + +
994A TYR* 1.3 62.7 + - - +
995A THR 3.1 0.9 + - - -
996A SER* 3.2 20.6 + - - +
999A LEU* 3.9 11.6 - - + +
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Residues in contact with TYR 994 (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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472A VAL* 3.8 19.2 - - + +
473A ASN* 4.0 28.3 + - - +
475A PHE* 4.1 20.9 - + - -
649A GLU* 4.4 20.6 + - + +
650A LEU* 4.1 26.2 - - + +
967A LEU* 3.7 35.5 - - + +
971A PHE* 3.9 18.6 - + + -
990A HIS 2.9 18.7 + - - +
991A HIS* 3.2 8.5 + + - +
993A LEU* 1.3 75.4 - - - +
995A THR* 1.3 61.8 + - + +
996A SER 3.8 0.3 + - - -
1000A GLN* 3.4 15.6 + - - +
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Residues in contact with THR 995 (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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569A ASP* 4.3 0.2 - - - +
649A GLU 4.0 11.7 - - - +
650A LEU 3.1 26.3 - - - +
651A CYS* 4.8 2.1 - - - -
652A CYS 3.9 12.3 - - - +
653A LYS* 3.2 33.2 + - - +
654A PRO* 3.8 17.4 - - + +
991A HIS* 3.3 19.3 - - + +
992A TRP* 2.6 23.5 + - - -
994A TYR* 1.3 80.3 - - + +
996A SER* 1.3 63.7 + - - +
997A LYS* 3.4 5.4 + - - +
1000A GLN* 3.1 5.2 + - - +
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Residues in contact with SER 996 (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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510A LEU* 4.5 16.2 - - - +
569A ASP* 3.1 20.6 + - - -
653A LYS* 3.8 4.9 - - - +
992A TRP* 3.3 9.0 + - - -
993A LEU* 3.2 13.3 + - - +
995A THR* 1.3 76.1 - - - +
997A LYS* 1.3 63.0 + - - +
998A TYR* 4.1 1.0 - - - +
999A LEU* 3.4 35.8 + - - +
1000A GLN* 3.2 22.2 + - - +
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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