Contacts of the helix formed by residues 938 - 950 (chain A) in PDB entry 4QMH
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 HIS 938 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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896A PRO 2.8 29.8 + - - -
898A ILE* 3.5 28.5 - - + +
899A GLY 5.9 0.9 - - - -
902A ALA* 3.5 20.9 - - + +
927A LEU* 5.4 2.0 - - + -
931A MET* 3.5 26.1 - - + -
934A GLY 4.1 1.3 - - - -
935A CYS* 3.1 8.5 + - - +
937A ASN* 1.3 94.5 + - + +
939A VAL* 1.3 64.5 + - - +
940A ARG 3.3 2.7 - - - -
941A ASN* 3.1 10.5 + - - +
942A LEU* 3.1 41.9 + - + +
968A PHE* 4.9 2.0 - - + -
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Residues in contact with VAL 939 (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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935A CYS 3.8 4.2 + - - +
936A ARG* 3.4 29.4 + - + +
937A ASN 3.6 0.2 - - - -
938A HIS* 1.3 77.8 - - - +
940A ARG* 1.3 60.4 + - - +
942A LEU* 5.0 1.6 - - - -
943A PHE* 2.8 44.5 + - + +
946A PHE* 6.5 0.4 - - - -
968A PHE* 4.0 19.1 - - + +
973A GLY 5.5 3.1 - - - +
976A GLU* 3.5 35.9 - - + +
977A PHE* 3.7 30.7 - - + -
982A MET* 4.4 2.7 - - + -
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Residues in contact with ARG 940 (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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936A ARG 5.0 0.2 + - - -
937A ASN 5.2 3.5 + - - +
938A HIS 3.3 0.6 - - - -
939A VAL* 1.3 79.6 - - - +
941A ASN* 1.3 64.4 + - - +
944A PRO* 3.4 18.7 - - - +
980A SER* 3.0 34.2 + - - -
982A MET* 4.3 15.2 - - + +
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Residues in contact with ASN 941 (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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902A ALA* 3.7 36.8 - - + +
903A PRO* 3.8 27.6 - - - +
906A ALA* 3.4 20.0 - - + +
937A ASN 5.4 1.6 + - - -
938A HIS* 3.1 14.5 + - - +
940A ARG* 1.3 82.9 - - - +
942A LEU* 1.3 62.1 + - + +
944A PRO* 3.9 6.8 - - - +
945A GLY 4.7 2.8 + - - -
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Residues in contact with LEU 942 (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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902A ALA* 3.6 26.9 - - + +
905A LEU* 3.9 19.1 - - + -
906A ALA 3.9 7.2 - - - +
909A LEU* 3.6 11.6 - - + +
924A CYS* 4.2 12.8 - - - -
927A LEU* 4.6 11.7 - - + -
938A HIS* 3.1 27.7 + - + +
939A VAL* 5.0 1.1 - - - -
941A ASN* 1.3 77.9 - - + +
943A PHE* 1.3 67.1 + - - +
944A PRO 3.4 2.5 - - - -
945A GLY* 3.0 5.8 + - - -
946A PHE* 3.0 38.3 + - + -
968A PHE* 3.8 27.8 - - + -
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Residues in contact with PHE 943 (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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939A VAL* 2.8 27.6 + - + +
942A LEU* 1.3 77.9 - - - +
944A PRO* 1.3 64.6 - - + +
946A PHE* 3.1 9.7 + + + -
947A LEU* 2.9 61.1 + - + +
965A ILE* 3.9 26.5 - - + -
977A PHE* 3.5 61.9 - + + -
982A MET* 3.6 23.6 - - + -
983A ILE* 3.9 13.5 - - + -
1001A TRP* 4.5 4.5 - + - -
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Residues in contact with PRO 944 (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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939A VAL 3.7 0.9 - - - +
940A ARG 3.4 25.1 - - - +
941A ASN 3.9 4.9 - - - +
942A LEU 3.6 3.1 - - - -
943A PHE* 1.3 93.4 - - + +
945A GLY* 1.3 55.4 + - - +
947A LEU* 3.4 11.6 + - + +
948A HIS* 3.0 28.6 + - - +
982A MET* 3.8 22.4 - - + +
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Residues in contact with GLY 945 (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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906A ALA* 5.3 2.5 - - - -
909A LEU* 4.1 26.6 - - - +
910A VAL* 4.4 10.3 - - - +
941A ASN 4.7 2.4 + - - -
942A LEU 3.0 8.9 + - - -
944A PRO* 1.3 76.7 - - - +
946A PHE* 1.3 66.4 + - - +
948A HIS* 3.3 7.3 + - - +
949A ALA* 3.1 22.9 + - - +
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Residues in contact with PHE 946 (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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909A LEU* 3.6 24.7 - - + -
921A LEU* 3.9 12.8 - - + -
924A CYS* 3.8 18.2 - - + -
939A VAL* 6.5 0.2 - - - -
942A LEU* 3.0 33.9 + - + -
943A PHE* 3.5 16.6 - + + +
945A GLY* 1.3 75.2 - - - +
947A LEU* 1.3 65.1 + - - +
949A ALA* 3.2 12.4 + - - -
950A LEU* 3.3 10.7 + - - +
961A ALA* 3.5 15.9 - - - +
964A CYS* 3.8 23.1 - - + -
965A ILE* 3.6 28.9 - - + -
968A PHE* 3.7 41.5 - + + -
977A PHE* 5.6 1.1 - + - -
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Residues in contact with LEU 947 (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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943A PHE* 2.9 61.4 + - + +
944A PRO* 3.6 8.7 - - + +
946A PHE* 1.3 77.0 - - - +
948A HIS* 1.3 63.9 + - - +
950A LEU* 3.1 31.7 + - + +
965A ILE* 4.1 3.4 - - + -
982A MET* 3.5 30.5 - - + +
983A ILE* 4.1 2.7 - - + -
986A ALA* 4.1 16.2 - - + -
994A LEU* 3.3 12.1 - - + +
998A LEU* 3.8 29.8 - - + -
1001A TRP* 5.8 0.2 - - + -
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Residues in contact with HIS 948 (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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909A LEU 6.0 0.4 - - - -
910A VAL* 4.3 23.6 - - + -
944A PRO 3.0 17.0 + - - +
945A GLY* 3.7 8.1 - - - +
946A PHE 3.2 0.4 - - - -
947A LEU* 1.3 77.9 - - - +
949A ALA* 1.3 62.1 + - - +
951A GLY* 3.1 15.4 + - - -
952A ASP 4.3 0.9 + - - -
986A ALA* 6.1 0.2 - - - -
994A LEU* 4.3 11.7 - - + +
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Residues in contact with ALA 949 (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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909A LEU 5.2 7.6 - - - +
921A LEU* 4.3 20.2 - - + -
945A GLY 3.1 13.0 + - - +
946A PHE 3.2 8.7 + - - +
948A HIS* 1.3 72.7 - - - +
950A LEU* 1.3 59.9 + - - +
951A GLY 3.0 6.1 - - - -
952A ASP* 3.1 25.2 + - - +
957A VAL* 4.2 6.2 - - + +
958A ARG* 3.9 8.0 - - - +
961A ALA* 3.7 16.4 - - + -
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Residues in contact with LEU 950 (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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946A PHE 3.3 12.1 + - - +
947A LEU* 3.1 28.3 + - + +
949A ALA* 1.3 76.5 - - - +
951A GLY* 1.3 55.4 + - - +
952A ASP 3.3 1.8 - - - -
958A ARG* 3.0 35.7 - - - +
961A ALA* 3.9 7.4 - - + -
962A LEU* 3.5 39.3 - - + +
965A ILE* 3.9 18.4 - - + -
993A ALA 3.7 0.3 - - - +
994A LEU* 3.7 10.9 - - + -
997A GLU* 3.6 27.7 - - + +
998A LEU* 4.3 19.1 - - + -
1001A TRP* 5.8 0.9 - - + -
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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
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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