Contacts of the helix formed by residues 638 - 648 (chain A) in PDB entry 4CEJ
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 GLN 638 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631A LYS* 3.4 29.6 - - - +
632A VAL* 5.0 1.0 - - + +
634A ASP* 5.0 1.6 - - - +
635A ASN* 3.1 20.5 - - - +
636A PRO 2.8 6.7 + - - +
637A TYR* 1.3 81.6 - - - +
639A ASP* 1.3 66.9 + - - +
640A ILE 3.2 2.5 + - - -
641A PRO* 3.2 26.5 - - + +
642A LEU* 3.1 22.3 + - - +
814B LYS 5.3 0.7 - - - -
816B ARG* 3.4 60.0 + - + +
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Residues in contact with ASP 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A TYR* 4.0 2.4 + - - -
638A GLN* 1.3 72.4 + - - +
640A ILE* 1.3 58.8 + - - +
642A LEU* 3.3 3.4 + - - +
643A ALA* 2.9 30.7 + - - +
662A ARG* 4.8 1.3 + - - -
669A PRO* 3.8 10.4 - - - +
670A TYR* 2.8 39.4 + - - +
671A TYR 4.4 1.0 + - - -
812B HIS 3.8 7.0 - - - +
813B LEU* 3.8 15.5 - - + +
814B LYS* 3.0 48.8 + - - +
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Residues in contact with ILE 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ASP* 1.3 73.9 - - - +
641A PRO* 1.3 75.6 - - + +
643A ALA* 4.5 1.6 - - - -
644A SER* 2.9 22.9 + - - -
813B LEU* 4.2 7.2 - - + +
814B LYS 4.1 2.4 + - - -
815B GLU* 3.8 41.3 - - + +
1125B ALA* 3.7 26.7 - - + +
1126B PHE* 3.7 33.2 - - + -
1128B SER* 3.6 19.5 - - - +
1129B VAL* 3.7 12.1 - - + +
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Residues in contact with PRO 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A SER* 3.6 24.7 - - - +
631A LYS* 4.1 28.3 - - + +
632A VAL* 3.8 13.0 - - + -
638A GLN* 3.2 33.0 - - + +
640A ILE* 1.3 98.3 - - + +
642A LEU* 1.3 60.0 + - - +
644A SER* 3.4 2.8 - - - -
645A VAL* 3.1 28.4 + - - +
1128B SER* 5.1 0.2 - - - +
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Residues in contact with LEU 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A VAL* 3.6 19.2 - - + +
636A PRO 4.3 5.2 - - - +
638A GLN 3.1 19.2 + - - +
639A ASP* 3.5 3.8 - - - +
641A PRO* 1.3 73.0 - - - +
643A ALA* 1.3 68.2 + - - +
645A VAL* 2.9 5.7 + - - +
646A LEU* 2.9 34.9 + - + +
670A TYR* 3.8 18.6 - - + +
671A TYR* 3.5 48.0 - - + +
674A MET* 4.5 8.3 - - + -
694A PHE* 3.9 31.0 - - + -
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Residues in contact with ALA 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ASP 2.9 20.0 + - - +
640A ILE 3.9 3.4 - - - +
642A LEU* 1.3 73.3 - - - +
644A SER* 1.3 57.3 + - - +
646A LEU* 3.6 3.7 - - - +
647A ARG* 3.0 32.2 + - - +
658A LEU* 4.7 4.6 - - + +
670A TYR* 4.1 16.5 - - + -
811B LEU* 5.2 3.1 - - + -
813B LEU* 3.6 32.8 - - + -
1129B VAL* 4.2 11.5 - - + +
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Residues in contact with SER 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A VAL* 4.2 7.3 - - - +
628A SER* 3.6 15.9 + - - -
640A ILE 2.9 18.4 + - - -
641A PRO 3.4 6.7 - - - -
643A ALA* 1.3 77.3 - - - +
645A VAL* 1.3 57.0 + - - +
648A SER* 3.1 15.2 + - - -
1128B SER* 2.3 46.5 + - - -
1129B VAL* 4.0 6.7 - - - +
1131B GLN* 3.0 23.0 + - - +
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Residues in contact with VAL 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A VAL* 4.2 2.2 - - - +
628A SER* 3.6 8.3 - - - +
629A VAL* 3.5 49.4 - - + +
632A VAL* 4.3 4.7 - - + -
641A PRO 3.1 14.3 + - - +
642A LEU* 2.9 8.3 + - - +
644A SER* 1.3 73.0 - - - +
646A LEU* 1.3 65.7 + - - +
648A SER* 2.6 25.9 + - - +
650A ILE* 4.5 5.2 - - + -
651A VAL* 3.7 10.3 - - + +
694A PHE* 3.5 37.5 - - + -
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Residues in contact with LEU 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A LEU* 2.9 23.6 + - + +
643A ALA 3.6 7.0 - - - +
645A VAL* 1.3 77.4 - - - +
647A ARG* 1.3 57.8 + - - +
651A VAL* 3.3 12.3 - - + +
652A GLY 3.1 11.8 + - - -
653A ALA* 3.0 27.5 + - + -
658A LEU* 3.8 10.5 - - + -
661A ILE* 3.8 20.6 - - + -
670A TYR* 3.5 34.8 - - + -
674A MET* 4.4 5.8 - - + -
691A LEU* 4.1 16.8 - - + -
694A PHE* 3.9 33.2 - - + -
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Residues in contact with ARG 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A ALA 3.0 17.2 + - - +
646A LEU* 1.3 72.1 - - - +
648A SER* 1.3 65.6 + - - +
649A PRO* 3.9 1.4 - - - +
652A GLY* 4.6 3.2 - - - -
653A ALA 3.6 19.2 - - - +
654A ASP* 5.6 0.2 - - - -
655A GLU* 2.9 18.2 + - - +
658A LEU* 4.1 17.2 - - + +
770B ASN* 3.0 30.1 + - - -
771B GLU 3.4 14.5 + - - -
772B VAL* 3.2 27.6 - - - +
803B PHE* 3.8 18.6 - - - -
1110B ILE* 3.8 8.6 - - - +
1129B VAL* 3.2 22.3 + - + +
1130B CYS 3.1 16.1 + - - -
1131B GLN* 3.9 14.0 + - - +
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Residues in contact with SER 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A VAL* 3.7 21.5 - - - -
644A SER 3.1 18.5 + - - -
645A VAL* 2.6 20.6 + - - -
646A LEU 3.2 0.4 - - - +
647A ARG* 1.3 79.1 - - - +
649A PRO* 1.3 62.5 - - - +
650A ILE* 3.0 23.3 + - - +
651A VAL 3.1 2.4 + - - -
652A GLY* 2.7 30.6 + - - -
1131B GLN* 3.7 10.1 - - - +
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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