Contacts of the helix formed by residues 752 - 762 (chain J) in PDB entry 4XLR
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 SER 752 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1051I GLU* 3.4 34.6 + - - +
1075I ASP* 3.7 8.4 + - - -
1076I VAL* 3.6 23.3 + - - +
1078I GLU* 4.5 3.8 + - - -
750J PRO 3.5 0.6 + - - -
751J LEU* 1.3 80.3 - - - +
753J SER* 1.3 55.1 + - - +
754J PHE* 3.1 13.3 + - - +
755J ALA* 2.9 13.4 + - - +
756J GLN* 2.5 34.0 + - - +
28K GLN* 4.1 1.2 + - - -
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Residues in contact with SER 753 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075I ASP* 2.5 28.0 + - - -
698J LYS* 4.1 15.1 + - - +
751J LEU 3.5 2.7 + - - -
752J SER* 1.3 73.8 + - - +
754J PHE* 1.3 57.8 + - - +
756J GLN* 3.5 10.2 - - - +
757J ALA* 2.9 27.4 + - - +
24K ALA* 4.5 5.1 - - - -
27K ALA* 5.6 3.1 - - - +
28K GLN* 3.9 18.4 - - - -
31K LEU* 4.0 17.0 - - - +
60K ALA* 5.3 5.1 - - - +
61K VAL* 4.7 6.6 - - - +
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Residues in contact with PHE 754 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047I HIS* 3.2 53.2 - + + -
752J SER* 3.1 8.4 + - - +
753J SER* 1.3 77.8 - - - +
755J ALA* 1.3 57.7 + - - +
757J ALA* 3.1 7.3 + - - +
758J GLU* 3.0 25.6 + - + +
1476J THR* 3.9 21.8 - - - -
1477J GLY* 5.7 0.7 - - - -
1482J ARG* 5.9 3.1 - - + -
20K THR* 4.5 3.1 - - + -
21K VAL* 4.1 26.7 - - + -
24K ALA* 3.4 30.3 - - + +
25K LYS* 4.7 17.5 - - + -
28K GLN* 3.8 15.6 - - - +
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Residues in contact with ALA 755 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047I HIS* 3.8 2.6 - - + +
1048I THR* 3.0 38.7 + - - +
1051I GLU* 3.9 19.3 - - + -
750J PRO* 3.6 9.9 - - + +
752J SER* 2.9 14.8 + - - +
754J PHE* 1.3 79.2 - - - +
756J GLN* 1.3 57.7 + - - +
758J GLU* 3.3 11.6 - - - +
759J ALA* 2.9 25.1 + - - +
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Residues in contact with GLN 756 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698J LYS* 3.3 46.0 - - + +
699J VAL 3.2 25.1 + - - +
749J VAL* 5.1 3.6 - - - +
750J PRO* 3.2 31.9 + - - +
751J LEU 4.7 1.6 - - - +
752J SER 2.5 19.0 + - - +
753J SER* 3.5 13.2 - - - +
755J ALA* 1.3 70.7 - - - +
757J ALA* 1.3 66.2 + - - +
759J ALA* 3.0 6.2 + - - +
760J ARG* 2.9 30.9 + - + +
61K VAL* 3.8 13.9 - - + -
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Residues in contact with ALA 757 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753J SER 2.9 14.4 + - - +
754J PHE 3.1 11.0 - - - +
756J GLN* 1.3 75.5 - - - +
758J GLU* 1.3 63.7 + - - +
760J ARG* 3.1 1.0 + - - +
761J ILE* 2.9 38.0 + - + +
20K THR* 4.0 6.1 - - + +
23K VAL* 3.8 27.8 - - + -
24K ALA* 4.0 12.1 - - - +
61K VAL* 4.5 9.1 - - + +
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Residues in contact with GLU 758 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045I ALA* 3.4 10.0 - - + +
1046I ALA 2.7 9.3 + - - -
1047I HIS* 2.5 30.6 + - - +
1048I THR* 2.4 38.9 + - - +
754J PHE* 3.0 14.9 + - + +
755J ALA* 3.3 5.7 - - - +
757J ALA* 1.3 76.7 - - - +
759J ALA* 1.3 62.0 + - - +
761J ILE 3.4 1.7 + - - -
762J GLN* 3.2 18.7 + - - +
763J MET* 3.2 21.9 + - - +
1476J THR* 2.4 31.9 + - + +
20K THR* 3.5 16.5 - - + +
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Residues in contact with ALA 759 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048I THR* 4.9 2.2 - - - +
699J VAL* 4.5 6.5 - - + +
701J LEU* 5.1 3.6 - - + -
715J ALA* 3.7 8.2 - - + +
750J PRO* 3.5 27.4 - - + -
755J ALA 2.9 14.5 + - - +
756J GLN* 3.0 14.7 + - - +
758J GLU* 1.3 76.6 - - - +
760J ARG* 1.3 58.2 + - - +
763J MET* 3.2 17.1 - - + -
764J LEU* 2.8 28.2 + - - -
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Residues in contact with ARG 760 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696J HIS* 6.3 0.2 - - - -
697J GLY* 3.5 23.2 + - - -
699J VAL* 3.4 35.9 - - + +
717J GLN* 4.9 4.6 - - - +
756J GLN* 2.9 23.9 + - - +
757J ALA 4.1 2.2 - - - +
759J ALA* 1.3 76.1 - - - +
761J ILE* 1.3 61.6 + - + +
764J LEU* 3.3 16.3 - - - +
767J HIS* 3.1 24.6 + - - -
3K GLU* 2.9 44.6 + - + +
59K ASN* 3.7 5.6 + - - -
61K VAL* 3.5 22.1 - - + +
62K THR* 3.3 42.2 + - - +
65K MET* 4.1 5.6 - - - +
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Residues in contact with ILE 761 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757J ALA* 2.9 31.3 + - + +
758J GLU 3.4 0.6 + - - -
760J ARG* 1.3 80.0 - - + +
762J GLN* 1.3 67.8 + - - +
767J HIS* 2.5 38.1 + - + +
6K ILE* 5.8 0.2 - - + -
10K PHE* 4.0 15.9 - - + -
16K LYS 4.5 0.9 - - - +
19K LEU* 4.0 25.4 - - + -
20K THR* 3.5 44.2 - - + +
23K VAL* 3.9 20.6 - - + -
65K MET* 4.8 12.1 - - + -
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Residues in contact with GLN 762 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043I TYR* 3.1 34.2 - - + +
1044I GLY 4.5 2.7 + - - -
1045I ALA* 4.9 1.1 - - - +
758J GLU* 3.2 32.9 + - - +
761J ILE* 1.3 80.2 - - + +
763J MET* 1.3 61.9 + - + +
764J LEU 3.3 2.2 - - - -
767J HIS* 4.8 1.1 - - - -
768J ASN* 2.8 26.9 + - - +
1476J THR* 3.7 7.6 - - - +
10K PHE* 5.3 1.3 - - - -
16K LYS* 3.4 37.8 - - - +
17K TYR* 3.1 28.2 - - - -
20K THR* 3.0 26.5 + - - -
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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