Contacts of the helix formed by residues 937 - 951 (chain C) in PDB entry 4OIP
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 ASP 937 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A PHE 3.8 1.2 - - - +
180A GLN* 3.6 20.0 - - - +
181A VAL* 2.7 26.1 + - - +
182A GLU* 4.9 0.2 - - - -
929C ARG* 5.1 0.4 - - - +
935C GLY 3.6 2.0 + - - -
936C VAL* 1.3 74.9 - - - +
938C LYS* 1.3 82.0 + - - +
939C ARG* 2.5 51.8 + - - +
940C GLU* 2.8 19.1 + - + +
941C VAL* 3.0 22.4 + - - +
975C TYR* 3.6 18.3 + - - +
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Residues in contact with LYS 938 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 5.0 3.2 - - - +
181A VAL* 3.1 22.1 + - + +
182A GLU* 4.2 0.4 - - - +
183A ASP* 3.3 38.4 - - + +
191A ASP* 3.2 27.2 + - - +
192A LEU 2.8 21.5 + - - -
193A ASP* 2.4 34.3 + - - +
936C VAL 4.0 0.4 + - - -
937C ASP* 1.3 85.4 + - - +
939C ARG* 1.3 58.2 + - + +
941C VAL* 3.0 13.9 + - + +
942C GLU* 2.9 27.9 + - - +
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Residues in contact with ARG 939 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.3 14.3 - - + +
179A PHE* 3.1 49.7 + - - -
181A VAL* 3.5 20.4 - - - +
860C HIS* 5.0 0.2 + - - -
937C ASP* 2.5 41.6 + - - -
938C LYS* 1.3 77.5 - - + +
940C GLU* 1.3 57.8 + - - +
942C GLU* 3.2 9.4 + - - +
943C VAL* 2.9 35.2 + - - +
975C TYR* 3.2 50.8 - - + +
980C GLY 3.4 15.1 + - - +
982C PRO* 3.6 27.5 - - + +
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Residues in contact with GLU 940 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862C PRO* 3.8 11.8 - - + +
925C TYR* 5.1 2.1 + - - -
926C PHE* 5.2 0.2 - - - -
929C ARG* 2.8 42.3 + - - -
936C VAL* 3.6 7.3 - - + +
937C ASP* 2.8 32.8 + - + +
939C ARG* 1.3 77.2 - - - +
941C VAL* 1.3 57.4 + - - +
943C VAL* 3.8 1.4 - - - +
944C LEU* 2.9 37.3 + - + +
963C LEU* 3.7 22.0 - - + +
973C VAL* 4.1 27.1 - - + +
975C TYR* 3.5 15.7 + - - +
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Residues in contact with VAL 941 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936C VAL* 4.5 17.7 - - + +
937C ASP 3.0 14.7 + - - +
938C LYS* 3.0 14.6 + - + +
940C GLU* 1.3 74.5 - - - +
942C GLU* 1.3 61.1 + - - +
944C LEU* 3.1 10.2 + - + +
945C ARG* 2.9 27.7 + - + +
959C PRO* 5.5 6.7 - - + -
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Residues in contact with GLU 942 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938C LYS 2.9 11.0 + - - +
939C ARG* 3.2 10.8 + - - +
941C VAL* 1.3 77.7 - - - +
943C VAL* 1.3 64.1 + - + +
945C ARG* 3.0 32.5 + - - +
946C ARG* 3.0 30.8 + - + +
982C PRO* 4.2 22.0 - - + +
984C GLU* 5.5 8.0 - - - +
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Residues in contact with VAL 943 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939C ARG 2.9 21.4 + - - +
940C GLU 3.8 3.8 - - - +
942C GLU* 1.3 76.0 - - + +
944C LEU* 1.3 57.3 + - - +
946C ARG* 3.3 2.8 + - - +
947C ALA* 2.9 27.4 + - - +
966C LEU* 5.0 3.1 - - + -
973C VAL* 4.0 29.4 - - + -
974C LEU 5.9 0.2 - - - +
982C PRO* 3.5 21.1 - - + -
983C ILE 3.5 20.2 - - - +
984C GLU* 4.0 12.1 - - - +
985C GLY 4.3 1.6 - - - -
986C PRO* 4.0 30.1 - - + -
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Residues in contact with LEU 944 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936C VAL* 6.1 0.2 - - + -
940C GLU* 2.9 27.9 + - + +
941C VAL* 3.1 10.1 + - - +
943C VAL* 1.3 74.6 - - + +
945C ARG* 1.3 59.6 + - - +
947C ALA* 3.8 2.6 - - - +
948C GLU* 2.9 35.1 + - - +
953C VAL* 4.1 5.5 - - + +
959C PRO* 3.7 35.0 - - + +
962C GLN* 3.6 37.0 - - + +
963C LEU* 3.7 27.6 - - + -
966C LEU* 3.9 19.7 - - + -
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Residues in contact with ARG 945 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941C VAL* 2.9 13.5 + - + +
942C GLU* 3.0 34.1 + - - +
944C LEU* 1.3 74.7 - - - +
946C ARG* 1.3 75.8 + - - +
948C GLU* 3.1 13.8 + - + +
949C LYS* 2.9 50.3 + - + +
796D ARG* 4.6 0.8 - - - +
856D GLY* 5.6 4.9 + - - -
859D ASP* 3.1 37.5 + - - -
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Residues in contact with ARG 946 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942C GLU* 3.0 23.0 + - + +
943C VAL 3.5 4.5 - - - +
945C ARG* 1.3 87.3 - - - +
947C ALA* 1.3 58.7 + - - +
949C LYS* 3.4 9.8 + - - +
950C LEU* 2.9 33.3 + - + +
984C GLU* 3.1 67.6 + - + +
985C GLY* 5.1 2.0 - - - -
791D TYR* 3.3 12.2 + - - -
796D ARG* 3.5 17.4 - - - +
859D ASP* 3.3 39.3 + - - +
860D LEU* 4.9 1.8 - - - +
861D GLN* 3.6 15.0 + - - -
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Residues in contact with ALA 947 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943C VAL 2.9 17.2 + - - +
944C LEU* 3.9 7.0 - - - +
946C ARG* 1.3 73.9 - - - +
948C GLU* 1.3 61.6 + - - +
950C LEU* 3.1 11.0 + - - +
951C GLY 2.9 23.6 + - - -
952C LEU* 3.0 17.2 + - + -
953C VAL* 3.8 7.8 + - + -
966C LEU* 4.2 27.8 - - + -
986C PRO* 4.2 11.6 - - + +
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Residues in contact with GLU 948 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944C LEU* 2.9 20.7 + - - +
945C ARG* 3.3 10.8 - - - +
947C ALA* 1.3 76.7 - - - +
949C LYS* 1.3 62.3 + - + +
951C GLY* 3.1 13.5 + - - -
953C VAL* 3.6 14.5 - - + +
955C PRO* 3.4 35.7 - - + +
956C GLY 4.5 1.7 + - - -
962C GLN* 3.2 37.9 + - - +
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Residues in contact with LYS 949 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945C ARG* 2.9 48.3 + - + +
946C ARG* 3.6 11.7 - - - +
948C GLU* 1.3 76.4 - - + +
950C LEU* 1.3 60.2 + - + +
951C GLY* 3.4 0.7 + - - -
796D ARG* 3.5 41.9 - - - +
798D GLU* 3.9 18.9 + - - +
823D LEU* 6.3 0.8 - - - +
1017D PHE* 6.1 1.0 - - - -
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Residues in contact with LEU 950 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946C ARG* 2.9 19.6 + - + +
947C ALA* 3.1 17.9 + - - +
949C LYS* 1.3 77.1 - - + +
951C GLY* 1.3 60.1 + - - +
952C LEU* 3.3 22.8 + - + +
985C GLY* 4.7 8.1 - - - -
986C PRO* 4.5 16.2 - - + -
946D GLY 5.8 2.0 - - - +
1014D ASN 5.6 0.3 - - - +
1015D TYR* 4.1 17.0 - - - +
1017D PHE* 3.6 41.1 - - + +
1018D ASN* 5.1 1.1 - - - +
1019D PRO* 6.3 0.9 - - + -
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Residues in contact with GLY 951 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947C ALA 2.9 3.2 + - - -
948C GLU 3.1 11.8 + - - -
949C LYS 3.2 1.7 - - - -
950C LEU* 1.3 80.2 - - - +
952C LEU* 1.3 64.9 + - - +
953C VAL 3.5 6.6 - - - -
1015D TYR* 4.2 19.4 - - - -
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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