Contacts of the helix formed by residues 628 - 635 (chain A) in PDB entry 4FWF
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 PRO 628 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ARG* 4.1 11.9 - - - +
627A VAL* 1.3 93.4 - - + +
629A LEU* 1.3 68.5 + - - +
630A ALA 4.2 0.4 - - - +
631A LEU* 3.0 17.2 + - + -
632A LEU* 3.3 8.7 + - - +
762A TRP 3.6 23.6 - - - +
763A ILE* 3.7 25.6 - - + +
765A MET* 3.7 11.0 - - + -
904A FAD 3.7 36.6 - - + +
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Residues in contact with LEU 629 (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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420A ARG* 5.2 0.6 - - - +
627A VAL 3.8 1.4 + - - -
628A PRO* 1.3 70.9 - - - +
630A ALA* 1.3 57.2 + - - +
632A LEU* 3.0 15.4 + - + +
633A GLN* 2.9 45.2 + - - +
651A ILE* 3.6 26.2 - - + +
654A LEU* 3.7 18.4 - - + -
655A GLY 3.4 35.2 - - - +
656A ALA* 3.7 4.7 - - - +
765A MET* 3.5 13.7 - - + -
768A SER* 4.1 8.5 - - - -
782A ILE* 4.2 19.1 - - + -
795A GLU* 5.1 1.0 + - - +
796A ALA* 4.0 22.1 - - + +
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Residues in contact with ALA 630 (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 PRO 3.1 0.8 - - - -
629A LEU* 1.3 80.2 - - - +
631A LEU* 1.3 58.4 + - - +
633A GLN* 3.5 8.9 + - - +
634A LYS* 3.0 33.7 + - + +
656A ALA* 3.8 20.2 - - + -
763A ILE 3.7 13.7 - - - +
764A GLN* 3.7 30.7 - - + +
765A MET* 3.5 4.3 - - - -
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Residues in contact with LEU 631 (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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627A VAL* 4.5 14.8 - - + -
628A PRO* 3.0 15.3 + - + +
630A ALA* 1.3 78.3 - - - +
632A LEU* 1.3 60.7 + - - +
633A GLN 3.2 0.2 - - - -
634A LYS* 3.8 3.4 - - + +
635A GLY 3.1 18.2 + - - -
636A ALA* 3.2 31.6 + - + +
637A ILE 4.7 0.9 + - - -
761A PRO 3.5 9.9 - - - +
762A TRP* 3.1 65.3 - - + +
763A ILE* 3.5 17.5 - - - +
764A GLN* 4.1 11.0 - - + +
904A FAD 4.2 4.9 - - - +
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Residues in contact with LEU 632 (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* 4.4 8.3 - - + -
627A VAL* 3.8 30.0 - - + +
628A PRO 3.3 8.4 + - - +
629A LEU* 3.0 15.9 + - + +
631A LEU* 1.3 75.9 - - - +
633A GLN* 1.3 63.4 + - - +
635A GLY* 3.2 13.8 + - - -
637A ILE* 5.9 2.2 - - + -
639A PHE* 4.3 23.1 - - + -
643A LEU* 5.0 2.4 - - + +
648A MET* 4.6 10.4 - - - +
651A ILE* 3.9 39.3 - - + +
782A ILE* 4.5 15.9 - - + -
792A PHE* 4.5 15.5 - - + -
796A ALA* 6.6 0.2 - - + -
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Residues in contact with GLN 633 (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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629A LEU* 2.9 31.9 + - + +
630A ALA* 3.6 7.0 - - - +
631A LEU 3.2 0.2 - - - -
632A LEU* 1.3 79.6 - - - +
634A LYS* 1.3 62.5 + - + +
635A GLY 3.5 0.3 + - - -
648A MET* 5.4 4.1 - - - +
651A ILE* 2.8 39.1 + - + +
652A ASN* 4.0 22.7 + - - +
654A LEU 2.8 23.7 + - - +
656A ALA* 4.1 17.3 + - - +
771A LYS* 4.8 3.4 + - - +
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Residues in contact with LYS 634 (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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630A ALA* 3.0 22.1 + - + +
631A LEU* 3.6 6.7 + - + +
632A LEU 3.3 0.2 - - - -
633A GLN* 1.3 77.4 - - + +
635A GLY* 1.3 63.5 + - - +
636A ALA* 3.4 7.2 + - + +
764A GLN* 4.0 26.5 - - - +
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Residues in contact with GLY 635 (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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631A LEU 3.1 4.9 + - - -
632A LEU* 3.2 11.8 + - - -
633A GLN 3.2 4.4 - - - -
634A LYS* 1.3 80.6 - - - +
636A ALA* 1.3 65.2 + - - +
637A ILE 3.1 15.5 + - - +
638A GLN* 5.3 0.5 - - - -
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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