Contacts of the strand formed by residues 711 - 716 (chain E) 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 HIS 711 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389E ILE 3.8 0.7 - - - +
390E ILE* 3.6 0.7 - - - -
391E ARG* 2.8 34.6 + - + +
393E GLY 2.5 35.7 + - - -
395E GLY* 3.2 19.1 + - - -
397E HIS* 5.4 4.3 - - - -
672E ASN* 3.6 24.4 + - - +
705E ASP* 2.9 23.3 - - - -
709E LYS* 3.0 21.8 - - + +
710E LEU* 1.2 87.6 - - - +
712E ILE* 1.3 66.5 + - - +
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Residues in contact with ILE 712 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLN* 4.3 11.9 - - - +
354E THR* 4.4 20.4 - - + +
356E LEU* 3.8 42.6 - - + -
388E ARG* 4.1 17.7 - - + +
389E ILE 3.3 7.0 - - - +
390E ILE* 3.7 22.4 - - + +
710E LEU 4.5 5.8 - - - +
711E HIS* 1.3 79.0 - - - +
713E ARG* 1.3 80.2 + - - +
714E THR* 4.9 0.9 - - - +
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Residues in contact with ARG 713 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E LEU 3.6 0.3 - - - +
388E ARG* 3.3 7.1 - - - -
389E ILE* 2.7 60.9 + - + +
391E ARG* 4.7 18.4 - - - +
712E ILE* 1.3 77.5 - - - +
714E THR* 1.3 72.2 + - - +
715E VAL* 4.9 3.3 - - - +
798E THR 5.4 0.4 + - - -
799E PHE* 5.9 0.2 - - - +
800E GLU* 4.4 22.2 + - - +
801E VAL* 3.5 30.4 - - - +
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Residues in contact with THR 714 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E ASP* 4.5 6.3 + - - +
354E THR* 5.0 2.1 + - - -
386E SER* 4.0 10.1 - - - -
387E LEU 3.6 2.0 - - - -
388E ARG* 3.0 45.4 + - - +
712E ILE* 4.9 1.2 - - - +
713E ARG* 1.3 84.3 + - - +
715E VAL* 1.3 75.5 + - - +
716E PRO* 4.1 13.1 - - + +
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Residues in contact with VAL 715 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E SER* 3.4 0.2 - - - -
387E LEU* 2.8 58.9 + - + +
389E ILE* 3.9 17.7 - - + -
713E ARG* 4.8 4.3 - - - +
714E THR* 1.3 83.1 - - - +
716E PRO* 1.3 71.9 - - + +
717E LEU* 3.7 6.2 + - + +
796E GLN* 5.5 1.1 - - + -
801E VAL* 3.4 48.0 - - + +
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Residues in contact with PRO 716 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E GLY 3.8 6.3 - - - +
386E SER* 4.3 5.2 - - - -
714E THR* 4.1 13.9 - - + +
715E VAL* 1.3 91.1 - - + +
717E LEU* 1.3 63.4 + - - +
718E TYR* 3.8 36.9 - - + +
756E ALA* 5.3 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