Contacts of the helix formed by residues 981 - 999 (chain A) in PDB entry 1MWH
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 981 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A PRO* 4.0 32.3 - - + +
448A GLN* 5.4 7.2 - - - +
978A LEU 4.6 1.8 + - - -
979A MET 3.3 7.8 - - - +
980A GLN* 1.3 82.0 - - + +
982A PRO* 1.3 70.9 - - - +
983A GLU* 2.7 39.7 + - - +
984A LEU* 3.2 20.6 + - + +
985A LYS 3.6 3.5 + - - -
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Residues in contact with PRO 982 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A MET 4.9 1.3 - - - +
980A GLN 3.4 9.6 - - - +
981A ASN* 1.3 88.8 - - - +
983A GLU* 1.3 59.0 + - - +
985A LYS* 3.4 9.0 + - + +
986A SER* 2.9 29.7 + - - +
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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
----------------------------------------------------------
445A PRO* 3.6 21.8 - - + +
981A ASN* 2.7 22.4 + - - +
982A PRO* 1.3 75.1 - - - +
984A LEU* 1.3 59.2 + - - +
986A SER* 3.6 8.3 + - - -
987A ARG* 3.2 54.4 + - + +
1151A GLN* 5.3 2.1 + - - +
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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
----------------------------------------------------------
445A PRO* 4.1 9.3 - - + +
446A LEU* 4.1 21.3 - - - +
449A ALA* 3.6 28.7 - - + -
978A LEU* 3.9 15.9 - - + +
979A MET* 4.2 8.3 - - + -
981A ASN* 3.2 15.8 + - + +
983A GLU* 1.3 76.9 - - - +
985A LYS* 1.3 66.8 + - - +
987A ARG* 2.9 18.7 + - - +
988A VAL* 3.0 17.1 + - - +
1009A LEU* 3.8 19.7 - - + -
1149A GLY* 3.6 39.3 - - - +
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Residues in contact with LYS 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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972A GLN* 6.0 2.4 - - - +
979A MET* 4.1 30.9 - - + +
981A ASN 3.6 4.7 + - - +
982A PRO* 3.4 13.8 + - + +
984A LEU* 1.3 78.4 - - - +
986A SER* 1.3 63.1 + - - +
988A VAL* 3.1 5.9 + - - +
989A LEU* 2.9 50.4 + - + +
1010A PHE* 4.6 16.4 - - + -
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Residues in contact with SER 986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982A PRO* 2.9 18.5 + - - +
983A GLU* 3.7 8.8 - - - -
984A LEU 3.2 0.2 - - - -
985A LYS* 1.3 78.8 - - - +
987A ARG* 1.3 62.4 + - - +
989A LEU* 3.9 10.4 - - - +
990A ARG* 3.0 24.4 + - - +
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Residues in contact with ARG 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP* 2.9 35.5 + - - -
445A PRO* 3.8 9.0 - - - +
446A LEU* 3.9 4.9 - - - +
983A GLU* 3.2 41.5 + - + +
984A LEU* 2.9 13.3 + - - +
986A SER* 1.3 79.1 - - - +
988A VAL* 1.3 57.7 + - - +
990A ARG* 3.1 9.0 + - - +
991A GLY 2.9 23.6 + - - -
1146A LEU* 3.6 17.7 - - + +
1149A GLY 2.7 37.2 + - - +
1150A LEU* 3.3 17.2 - - - +
1151A GLN* 3.5 41.5 - - - +
1152A GLU 5.5 0.4 - - - +
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Residues in contact with VAL 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A MET* 4.1 6.5 - - + -
984A LEU 3.0 11.8 + - - +
985A LYS 3.7 4.7 - - - +
987A ARG* 1.3 75.0 - - - +
989A LEU* 1.3 57.3 + - - +
991A GLY* 3.1 2.8 + - - -
992A ARG* 2.9 27.3 + - - +
1008A SER* 4.0 7.0 - - - +
1009A LEU* 3.8 30.5 - - + -
1010A PHE* 3.5 41.3 - - + +
1146A LEU 3.6 11.2 - - - +
1147A MET* 3.8 22.9 - - + +
1149A GLY* 4.4 2.0 - - - +
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Residues in contact with LEU 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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985A LYS* 2.9 46.0 + - + +
986A SER* 3.9 8.1 - - - +
988A VAL* 1.3 72.7 - - - +
990A ARG* 1.3 68.0 + - - +
992A ARG* 2.9 26.5 + - + +
993A SER* 3.0 16.7 + - - -
1010A PHE* 3.8 26.5 - - + -
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Residues in contact with ARG 990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A SER 3.0 16.0 + - - +
987A ARG* 3.3 12.1 - - - +
989A LEU* 1.3 75.5 - - - +
991A GLY* 1.3 63.1 + - - +
993A SER* 3.4 9.5 + - - +
994A GLU* 3.0 65.3 + - - +
1142A THR* 6.2 0.4 - - - +
1146A LEU* 4.4 11.3 - - + +
1152A GLU* 3.1 39.5 + - + +
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Residues in contact with GLY 991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987A ARG 2.9 10.3 + - - -
988A VAL 3.1 4.2 + - - -
989A LEU 3.1 0.2 - - - -
990A ARG* 1.3 78.1 - - - +
992A ARG* 1.3 50.3 + - - +
994A GLU* 3.1 7.4 + - - +
995A TRP* 2.6 36.0 + - - +
1143A ALA* 3.7 5.9 - - - +
1146A LEU* 3.6 23.7 - - - +
1147A MET* 3.5 13.6 - - - +
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Residues in contact with ARG 992 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988A VAL* 2.9 10.9 + - - +
989A LEU* 2.9 20.8 + - + +
991A GLY* 1.3 71.9 - - - +
993A SER* 1.3 62.0 + - - +
994A GLU 3.0 4.0 - - - -
995A TRP* 3.0 17.1 + - + +
996A GLU* 3.2 19.6 + - - +
1008A SER* 5.2 0.2 - - - -
1010A PHE* 3.3 48.1 - - - +
1147A MET* 3.4 25.3 - - + +
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Residues in contact with SER 993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A LEU 3.0 12.8 + - - -
990A ARG* 3.4 14.7 + - - -
992A ARG* 1.3 75.9 - - - +
994A GLU* 1.3 63.5 + - - +
996A GLU* 3.8 13.2 + - - +
997A LYS* 3.5 34.0 + - - +
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Residues in contact with GLU 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990A ARG* 3.0 61.8 + - - +
991A GLY* 3.3 6.5 - - - +
992A ARG 3.0 0.4 - - - -
993A SER* 1.3 80.4 + - - +
995A TRP* 1.3 63.8 + - - +
996A GLU 3.2 0.2 - - - -
997A LYS* 3.3 13.5 + - - +
998A TYR* 3.2 56.3 + - - +
1139A LYS* 4.2 17.0 - - - +
1142A THR* 5.2 3.8 - - - +
1143A ALA* 3.7 14.4 - - + +
1146A LEU* 4.6 6.1 - - + +
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Residues in contact with TRP 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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991A GLY 2.6 19.5 + - - +
992A ARG* 3.0 6.9 + - + +
994A GLU* 1.3 75.2 - - - +
996A GLU* 1.3 66.9 + - - +
999A GLY* 2.9 35.9 + - - +
1000A ALA* 2.8 43.6 + - + +
1003A ILE* 3.5 21.9 + - + -
1006A PRO* 3.1 35.3 - - + +
1131A LEU* 3.5 40.8 - - + -
1140A ALA 3.8 7.2 - - - -
1143A ALA* 4.0 15.5 - - + -
1144A GLN* 4.2 15.9 - - + -
1147A MET* 3.8 21.1 - - + -
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Residues in contact with GLU 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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992A ARG* 3.2 14.5 + - - +
993A SER* 3.9 12.8 - - - +
994A GLU 3.2 0.8 - - - -
995A TRP* 1.3 90.0 - - - +
997A LYS* 1.3 63.9 + - + +
1000A ALA* 4.0 23.6 + - - +
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Residues in contact with LYS 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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993A SER* 3.5 27.4 + - - +
994A GLU* 3.3 11.3 + - - +
995A TRP 3.3 0.2 - - - -
996A GLU* 1.3 82.2 - - + +
998A TYR* 1.3 89.9 + - + +
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Residues in contact with TYR 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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994A GLU* 3.2 43.5 + - - +
997A LYS* 1.3 101.5 - - + +
999A GLY* 1.3 59.6 + - - +
1000A ALA 4.0 0.9 - - - -
1002A ILE* 3.0 20.4 - - - +
1136A ALA* 4.8 0.2 - - - +
1137A ASP* 4.1 13.5 + - + +
1139A LYS* 3.4 52.0 + - + +
1140A ALA* 3.6 26.5 - - + +
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Residues in contact with GLY 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995A TRP* 2.9 54.7 + - - +
998A TYR* 1.3 75.4 - - - +
1000A ALA* 1.3 63.9 + - - +
1001A GLY 3.5 0.3 + - - -
1002A ILE* 3.2 26.5 + - - +
1003A ILE 3.9 0.2 + - - -
1131A LEU* 4.7 0.2 - - - -
1140A ALA* 4.1 5.5 - - - +
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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