Contacts of the strand formed by residues 973 - 978 (chain C) in PDB entry 3EI4
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 973 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968C ALA* 3.1 19.6 - - - +
969C GLU* 2.7 40.1 + - - +
971C ALA* 3.5 3.1 - - - +
972C PHE* 1.3 75.3 - - - +
974C LEU* 1.3 68.1 + - - +
998C PHE 3.2 5.2 - - - +
999C HIS* 2.9 37.2 - - - +
1076C PHE* 3.1 37.1 - - + -
1077C HIS 2.8 28.6 + - - +
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Residues in contact with LEU 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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6C VAL* 4.5 9.9 - - + -
966C LEU* 4.0 7.6 - - + -
967C GLY 3.0 7.9 - - - +
968C ALA* 3.5 27.6 - - + -
973C ASN* 1.3 78.2 - - - +
975C PHE* 1.3 63.5 + - - +
996C GLY 4.2 0.7 - - - -
997C LEU* 3.4 6.9 - - - +
998C PHE* 2.7 55.5 + - + +
1000C LEU* 3.9 28.3 - - + -
1004C VAL* 4.6 1.1 - - + -
1007C PHE* 4.2 15.9 - - + -
1030C PHE* 5.5 3.6 - - + -
1040C VAL* 5.2 4.0 - - + -
1076C PHE* 4.3 2.6 - - - -
1088C PHE* 4.0 27.6 - - + -
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Residues in contact with PHE 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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930C VAL* 4.0 23.1 - - + -
952C ASN* 3.5 50.7 - - + +
954C MET* 3.9 15.3 - - + -
965C PHE 5.2 0.4 - - - -
966C LEU* 3.1 7.3 - - - +
967C GLY* 2.7 67.7 + - - -
968C ALA* 3.8 2.9 - - - -
969C GLU* 4.1 20.2 - - + -
974C LEU* 1.3 76.7 - - - +
976C VAL* 1.3 64.8 + - - +
977C CYS* 4.5 8.7 - - - -
994C GLU* 4.0 15.3 - - - +
996C GLY 3.0 8.5 - - - +
997C LEU* 4.1 13.2 - - + -
1076C PHE* 5.2 2.9 - + + -
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Residues in contact with VAL 976 (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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2C SER* 3.7 20.6 - - - +
4C ASN* 3.6 24.2 - - - +
960C LEU* 4.5 3.8 - - + -
964C ASN* 3.9 13.7 - - + +
965C PHE 3.0 9.0 - - - +
966C LEU* 4.0 9.9 - - + -
975C PHE* 1.3 80.9 - - - +
977C CYS* 1.3 70.7 + - - +
994C GLU* 3.1 4.3 - - - -
995C VAL* 2.5 35.5 + - + -
996C GLY* 2.9 18.3 + - - +
1088C PHE* 3.7 20.2 - - + -
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Residues in contact with CYS 977 (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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930C VAL* 3.5 30.5 - - + -
948C ASP* 3.7 25.8 - - - -
963C ASP 4.0 1.6 - - - -
964C ASN* 3.4 3.6 - - - -
965C PHE* 2.8 46.2 + - + -
975C PHE* 4.5 8.5 - - - -
976C VAL* 1.3 78.5 - - - +
978C GLN* 1.3 72.6 + - - +
992C LEU* 4.2 10.3 - - + -
993C GLN 3.1 6.5 - - - +
994C GLU* 4.2 6.7 - - - -
995C VAL* 4.3 0.2 - - - -
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Residues in contact with GLN 978 (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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1C MET* 4.0 8.7 - - - +
2C SER* 3.8 10.3 - - - -
946C ALA* 5.5 0.2 - - - +
963C ASP* 3.3 5.8 - - + -
964C ASN* 2.7 40.2 + - - +
977C CYS* 1.3 81.6 + - - +
979C LYS* 1.3 73.0 + - - +
991C HIS 3.9 3.1 - - - +
992C LEU* 3.2 29.5 - - - +
993C GLN* 2.6 26.2 + - + +
995C VAL* 3.3 36.0 - - + +
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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