Contacts of the helix formed by residues 962 - 975 (chain C) in PDB entry 4UVL
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 962 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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958C LEU* 4.1 16.1 - - + +
959C SER* 2.9 27.1 + - - +
961C ASP* 1.3 77.3 - - - +
963C LYS* 1.3 67.2 + - - +
964C GLU* 2.8 38.0 + - - +
965C PHE* 3.1 7.3 + - + +
966C GLN* 3.1 21.9 + - - +
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Residues in contact with LYS 963 (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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961C ASP 3.6 3.8 + - - +
962C ASP* 1.3 73.4 + - - +
964C GLU* 1.3 56.9 + - - +
966C GLN* 3.3 17.2 + - - +
967C SER* 2.9 30.3 + - - -
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Residues in contact with GLU 964 (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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958C LEU* 3.9 22.4 - - + +
962C ASP* 2.8 23.7 + - - +
963C LYS* 1.3 70.5 - - - +
965C PHE* 1.3 63.0 + - - +
967C SER* 2.8 22.4 + - - +
968C VAL* 3.2 16.3 + - - +
999C LYS* 3.1 25.3 - - - +
1151C TYR* 2.5 34.6 + - + +
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Residues in contact with PHE 965 (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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958C LEU* 3.6 36.3 - - + +
959C SER 3.1 22.7 - - - +
960C PRO* 3.7 33.4 - - + -
962C ASP* 3.1 5.5 + - + +
964C GLU* 1.3 77.4 - - - +
966C GLN* 1.3 63.8 + - + +
968C VAL 3.3 1.6 + - - -
969C GLU* 2.9 49.4 + - + -
994C ILE* 3.9 24.0 - - + -
995C LEU 5.5 1.3 - - - -
996C LYS* 4.5 4.5 - - - -
997C ILE* 3.7 40.6 - - + +
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Residues in contact with GLN 966 (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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960C PRO 2.8 26.8 + - - +
961C ASP* 3.5 19.8 + - - +
962C ASP 3.1 7.7 + - - +
963C LYS* 3.6 19.0 - - - +
964C GLU 3.2 0.4 - - - -
965C PHE* 1.3 83.1 - - + +
967C SER* 1.3 55.9 + - - +
969C GLU* 3.5 4.6 + - - +
970C GLU* 3.0 28.8 + - - +
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Residues in contact with SER 967 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963C LYS 2.9 13.8 + - - -
964C GLU* 2.8 25.8 + - - +
966C GLN* 1.3 73.6 - - - +
968C VAL* 1.3 67.0 + - - +
970C GLU* 3.4 4.8 + - - +
971C GLU* 3.0 25.3 + - - +
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Residues in contact with VAL 968 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964C GLU* 3.2 17.2 + - + +
965C PHE 3.7 3.1 - - - +
967C SER* 1.3 78.6 + - - +
969C GLU* 1.3 66.1 + - - +
971C GLU* 3.2 6.8 + - - +
972C MET* 3.0 21.7 + - - +
997C ILE* 3.8 21.3 - - + -
1030C PHE* 5.2 0.4 - - + -
1098C PHE* 4.2 19.7 - - + -
1151C TYR* 4.0 37.5 - - + +
1153C ILE* 3.7 28.3 - - + -
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Residues in contact with GLU 969 (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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965C PHE* 2.9 41.0 + - + +
966C GLN* 3.9 6.2 - - - +
968C VAL* 1.3 76.1 - - - +
970C GLU* 1.3 58.9 + - - +
972C MET* 3.2 8.5 + - - +
973C GLN* 2.8 57.6 + - + +
994C ILE* 3.7 23.3 + - + +
997C ILE* 3.9 5.0 - - + +
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Residues in contact with GLU 970 (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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966C GLN 3.0 17.7 + - - +
967C SER* 3.4 6.7 + - - +
968C VAL 3.2 0.2 - - - -
969C GLU* 1.3 77.7 - - - +
971C GLU* 1.3 52.2 + - - +
973C GLN* 4.3 10.7 - - - +
974C SER* 2.6 60.4 + - - +
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Residues in contact with GLU 971 (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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967C SER 3.0 16.5 + - - +
968C VAL* 3.2 5.8 + - - +
970C GLU* 1.3 78.2 - - - +
972C MET* 1.3 55.2 + - - +
974C SER* 3.8 4.7 + - - -
975C THR* 2.8 53.6 + - - +
1028C MET 5.9 0.2 - - - +
1030C PHE* 3.9 12.1 - - + -
1063C GLU 5.2 1.0 - - - +
1098C PHE* 3.7 32.3 - - + -
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Residues in contact with MET 972 (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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968C VAL* 3.0 16.1 + - + +
969C GLU* 3.3 10.8 - - - +
971C GLU* 1.3 79.0 - - - +
973C GLN* 1.3 63.1 + - + +
975C THR* 3.4 3.1 + - - -
976C VAL* 3.7 0.7 - - - +
992C TYR* 3.4 32.6 - - + -
994C ILE* 3.5 30.1 - - + -
1030C PHE* 3.7 20.1 - - + -
1065C SER* 2.7 25.9 + - - -
1096C LEU* 3.7 24.0 - - + -
1153C ILE* 3.8 31.6 - - + -
1155C TYR* 4.0 15.0 - - + -
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Residues in contact with GLN 973 (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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969C GLU* 2.8 53.9 + - + +
970C GLU* 4.2 11.9 - - - +
972C MET* 1.3 73.7 - - + +
974C SER* 1.3 63.3 + - - +
975C THR 3.3 1.2 + - - -
976C VAL* 3.5 19.1 + - - +
990C ASN 4.9 2.8 - - - +
991C ARG* 3.5 13.4 - - + +
992C TYR* 2.9 54.3 + - - -
994C ILE* 4.1 5.4 - - - +
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Residues in contact with SER 974 (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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970C GLU* 2.6 48.4 + - - +
971C GLU* 3.6 10.0 + - - -
973C GLN* 1.3 74.1 - - - +
975C THR* 1.3 67.5 + - - +
976C VAL 3.4 4.9 + - - +
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Residues in contact with THR 975 (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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971C GLU* 2.8 40.2 + - + +
973C GLN 3.2 1.2 - - - -
974C SER* 1.3 87.2 - - - +
976C VAL* 1.3 59.3 + - - +
977C ARG 3.6 0.2 + - - -
1030C PHE* 3.7 1.7 - - - -
1063C GLU 3.4 21.7 + - - +
1064C ASN* 2.9 33.4 + - - +
1065C SER* 3.0 26.2 + - - -
1066C SER* 3.8 0.3 + - - -
1136C LEU* 4.5 11.4 - - + -
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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