Contacts of the helix formed by residues 982 - 995 (chain A) in PDB entry 5IYB
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 ASN 982 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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902A GLU* 2.8 40.2 + - - +
903A PHE 4.9 3.2 + - - -
904A GLN* 3.8 23.2 - - - +
980A PRO 3.9 0.2 - - - -
981A CYS* 1.3 67.4 - - - +
983A LEU* 1.3 60.5 + - - +
984A LEU* 3.5 16.8 + - - +
985A ARG* 3.3 35.2 + - - +
986A MET* 2.8 35.2 + - - +
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Residues in contact with LEU 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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904A GLN* 3.6 5.4 + - - +
981A CYS* 2.9 21.5 + - + +
982A ASN* 1.3 71.2 + - - +
984A LEU* 1.3 61.5 + - - +
986A MET* 3.9 3.7 - - - +
987A ILE* 2.9 37.1 + - + +
1041A PHE* 4.8 6.3 - - + -
1044A HIS* 3.7 34.1 - - + +
1045A LEU* 3.6 32.8 - - + -
1048A THR* 4.3 17.0 - - + +
1049A LEU* 4.5 5.8 - - + -
1068A LEU* 6.3 0.2 - - - -
1072A ILE* 3.7 40.2 - - + -
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Residues in contact with LEU 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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904A GLN* 5.0 2.0 + - - +
905A ASN* 5.8 10.5 - - + +
982A ASN* 3.4 8.4 + - - +
983A LEU* 1.3 77.8 - - - +
985A ARG* 1.3 57.4 + - - +
987A ILE* 3.4 4.7 + - - +
988A TRP* 2.8 31.7 + - - +
1044A HIS* 6.3 3.4 - - + +
1048A THR* 4.1 21.8 - - + -
1053A ARG* 5.0 5.6 - - - +
1058A PHE* 4.2 20.1 - - + -
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Residues in contact with ARG 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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601A ASN* 4.8 16.8 - - + +
602A CYS* 5.2 1.1 - - - +
655A ILE* 3.7 44.4 + - - +
658A LEU* 4.3 16.2 - - - +
659A GLU* 2.9 33.1 + - - +
902A GLU* 3.0 26.3 + - - -
982A ASN* 3.3 34.5 + - - +
984A LEU* 1.3 76.2 - - - +
986A MET* 1.3 62.3 + - - +
988A TRP* 3.6 7.7 - - + +
989A ASN* 2.7 45.7 + - - +
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Residues in contact with MET 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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659A GLU* 5.3 5.4 - - - +
981A CYS* 4.1 26.5 - - + +
982A ASN* 2.8 26.9 + - + +
983A LEU* 3.9 5.2 - - - +
985A ARG* 1.3 80.0 - - - +
987A ILE* 1.3 59.4 + - - +
989A ASN* 3.0 16.6 + - - +
990A ALA* 2.8 28.2 + - - +
1067A TRP* 4.2 2.6 - - + -
1068A LEU* 3.9 17.3 - - + +
1071A GLU* 3.9 21.8 - - + +
1072A ILE* 4.3 17.9 - - + -
1075A LYS* 3.7 42.4 - - + -
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Residues in contact with ILE 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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983A LEU* 2.9 28.6 + - - +
984A LEU* 3.7 5.2 - - - +
986A MET* 1.3 72.5 - - - +
988A TRP* 1.3 63.9 + - - +
990A ALA* 3.2 6.2 + - - +
991A GLN* 3.2 24.0 + - + +
1048A THR* 4.1 7.0 - - + -
1049A LEU* 3.8 23.8 - - + -
1054A MET* 4.1 2.7 - - + -
1058A PHE* 3.4 64.2 - - + -
1060A LEU* 4.1 8.5 - - + -
1068A LEU* 3.9 26.2 - - + -
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Residues in contact with TRP 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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601A ASN* 3.0 48.2 - - + -
603A ILE* 3.1 35.6 - - + +
629A VAL* 6.2 1.3 - - + -
630A VAL 3.9 4.9 - - - -
631A GLU* 3.2 51.6 - - + -
984A LEU 2.8 18.2 + - - +
985A ARG* 3.6 8.5 - - + +
987A ILE* 1.3 79.5 - - - +
989A ASN* 1.3 60.4 + - - +
991A GLN* 3.5 21.6 + - - +
992A LYS* 3.2 24.1 + - + -
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Residues in contact with ASN 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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599A HIS* 5.7 4.0 - - + -
601A ASN* 2.2 47.7 + - - +
659A GLU* 2.8 30.0 + - - +
985A ARG* 2.7 34.0 + - - +
986A MET* 3.0 21.4 + - - +
988A TRP* 1.3 71.8 - - - +
990A ALA* 1.3 61.8 + - - +
992A LYS* 3.5 3.1 + - - +
993A ILE* 3.2 30.9 + - + +
1067A TRP* 4.4 15.1 - - + -
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Residues in contact with ALA 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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986A MET 2.8 14.9 + - - +
987A ILE* 3.5 9.2 - - - +
989A ASN* 1.3 70.8 - - - +
991A GLN* 1.3 64.9 + - - +
993A ILE* 3.4 0.4 + - - -
994A PHE* 3.2 35.9 + - + +
1060A LEU* 3.8 24.9 - - + -
1064A ALA* 4.4 9.6 - - + +
1067A TRP* 4.0 24.3 - - + -
1068A LEU* 4.7 3.1 - - + -
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Residues in contact with GLN 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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987A ILE* 3.2 9.2 + - - +
988A TRP* 3.8 27.9 + - - +
989A ASN 3.4 0.2 - - - -
990A ALA* 1.3 78.4 - - - +
992A LYS* 1.3 61.4 + - - +
995A HIS* 3.2 17.8 + - - -
996A ILE* 3.3 28.7 + - + +
998A PRO* 5.5 8.7 - - - +
1057A GLU 4.2 5.1 + - - -
1058A PHE* 2.7 38.0 + - - +
1059A ARG* 4.8 2.8 - - - +
1060A LEU* 3.5 22.4 - - + -
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Residues in contact with LYS 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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598A GLY 4.5 0.8 + - - -
599A HIS* 2.9 51.6 + - - +
601A ASN* 3.3 24.3 + - - +
631A GLU* 5.2 5.8 - - + +
632A ASN* 3.3 40.9 + - + +
988A TRP* 3.2 20.6 + - + +
989A ASN* 3.7 8.5 - - - +
990A ALA 3.2 0.2 - - - -
991A GLN* 1.3 79.7 - - - +
993A ILE* 1.3 77.2 + - - +
995A HIS* 3.0 26.5 + - - -
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Residues in contact with ILE 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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599A HIS* 4.1 22.9 - - + +
989A ASN* 3.2 18.4 + - + +
990A ALA 3.4 0.2 + - - -
992A LYS* 1.3 88.6 - - - +
994A PHE* 1.3 80.4 + - + +
995A HIS* 3.1 24.0 + - - -
1067A TRP* 4.1 29.2 - - + -
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Residues in contact with PHE 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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990A ALA 3.2 20.5 + - - +
993A ILE* 1.3 92.2 - - + +
995A HIS* 1.3 71.0 + - - +
996A ILE* 3.6 23.4 + - + +
1061A SER* 4.6 1.6 - - - -
1063A GLU* 3.9 25.1 - - + -
1064A ALA* 3.6 41.1 - - + -
1067A TRP* 3.6 41.3 - + + -
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Residues in contact with HIS 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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632A ASN* 6.0 2.9 - - - -
991A GLN 3.2 7.9 + - - -
992A LYS 3.0 18.3 + - - -
993A ILE* 3.1 15.9 + - - -
994A PHE* 1.3 80.7 - - - +
996A ILE* 1.3 62.6 + - - +
997A ASN* 3.5 3.5 + - - +
138H ASP* 5.4 10.6 + - - -
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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