Contacts of the helix formed by residues 691 - 702 (chain A) in PDB entry 4YFI
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 691 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560A LEU* 4.2 21.1 - - + -
659A LEU* 4.6 8.5 - - + -
689A SER 3.6 6.5 - - - +
690A ILE* 1.3 94.2 - - + +
692A LYS* 1.3 66.2 + - - +
693A PRO* 4.1 9.2 - - + -
694A ILE* 3.2 28.5 + - + +
695A SER* 3.1 17.8 + - - -
722A CYS* 6.4 0.4 - - - -
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Residues in contact with LYS 692 (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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690A ILE 3.6 1.4 + - - +
691A PRO* 1.3 71.8 - - - +
693A PRO* 1.3 66.5 - - + +
695A SER* 2.8 20.9 + - - -
696A SER* 2.8 19.7 + - - -
676C ASP* 2.6 38.4 + - - -
680C HIS* 3.8 38.2 + - + +
682C ILE* 3.8 17.3 - - + +
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Residues in contact with PRO 693 (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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691A PRO* 3.5 11.4 - - + -
692A LYS* 1.3 95.9 - - + +
694A ILE* 1.3 57.3 + - - +
696A SER* 3.8 8.6 - - - -
697A LEU* 3.4 29.2 + - - +
718A LYS* 5.3 10.1 - - + +
722A CYS* 3.7 28.0 - - - -
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Residues in contact with ILE 694 (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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560A LEU* 4.6 4.5 - - + -
564A LEU* 3.9 32.1 - - + -
655A LEU* 4.2 16.2 - - + -
659A LEU* 3.1 42.8 - - + -
690A ILE* 4.0 5.4 - - + -
691A PRO* 3.2 35.1 + - + +
692A LYS 3.1 0.6 - - - -
693A PRO* 1.3 78.5 - - - +
695A SER* 1.3 60.8 + - - +
696A SER 3.2 0.9 - - - -
697A LEU* 3.1 8.1 + - - +
698A LEU* 2.9 28.4 + - + +
719A LEU* 4.8 7.4 - - + -
722A CYS* 4.7 13.5 - - + -
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Residues in contact with SER 695 (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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686A ILE* 3.9 24.2 - - - -
690A ILE* 4.0 8.5 + - - +
691A PRO 3.1 10.3 + - - -
692A LYS* 2.8 27.0 + - - -
694A ILE* 1.3 77.8 - - - +
696A SER* 1.3 54.7 + - - +
698A LEU* 3.2 11.9 + - - +
699A ILE* 2.9 38.3 + - - +
682C ILE* 3.8 22.3 - - - +
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Residues in contact with SER 696 (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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692A LYS 2.8 16.5 + - - -
693A PRO* 3.8 9.9 + - - -
695A SER* 1.3 76.3 + - - +
697A LEU* 1.3 62.6 + - - +
699A ILE* 3.5 5.0 + - - +
700A ARG* 3.2 47.6 + - - +
718A LYS* 5.9 1.6 - - - +
680C HIS* 4.9 22.0 - - - -
682C ILE* 5.7 0.4 - - - +
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Residues in contact with LEU 697 (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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652A ALA* 5.1 1.1 - - - +
655A LEU* 4.5 13.2 - - + -
693A PRO 3.4 15.4 + - - +
694A ILE* 3.1 11.9 + - - +
696A SER* 1.3 80.4 - - - +
698A LEU* 1.3 53.5 + - - +
700A ARG* 4.0 16.7 - - - +
701A GLY* 2.7 33.8 + - - -
710A PRO* 4.4 9.3 - - + +
714A GLU* 5.2 0.4 - - - +
715A VAL* 4.2 35.7 - - + +
718A LYS* 4.1 26.0 - - + -
719A LEU* 3.8 34.1 - - + -
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Residues in contact with LEU 698 (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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652A ALA* 3.2 31.6 - - - +
655A LEU* 3.9 15.7 - - + -
656A TRP* 3.7 40.2 - - + +
659A LEU* 4.7 0.7 - - + -
686A ILE* 4.4 10.3 - - + -
690A ILE* 4.6 10.8 - - + -
694A ILE* 2.9 28.3 + - + +
695A SER* 3.2 14.3 + - - +
697A LEU* 1.3 73.7 - - - +
699A ILE* 1.3 66.6 + - - +
701A GLY 3.1 0.3 + - - -
702A TRP* 3.0 49.4 + - + -
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Residues in contact with ILE 699 (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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686A ILE* 3.7 22.4 - - + -
695A SER* 2.9 25.1 + - - +
696A SER* 4.0 4.3 - - - +
698A LEU* 1.3 74.6 - - - +
700A ARG* 1.3 64.7 + - + +
702A TRP* 3.8 11.1 - - - +
703A ASN* 3.5 19.1 + - - +
680C HIS 4.3 6.3 - - - +
681C HIS* 3.5 42.6 - - + +
682C ILE* 4.2 13.7 - - + -
683C ARG* 5.2 1.3 - - + +
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Residues in contact with ARG 700 (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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696A SER* 3.2 33.5 + - - +
697A LEU* 4.0 16.8 - - - +
698A LEU 3.1 0.2 - - - -
699A ILE* 1.3 80.2 - - + +
701A GLY* 1.3 65.8 + - - +
702A TRP 3.2 2.0 - - - -
703A ASN* 3.1 24.1 - - - +
708A GLY 4.0 9.7 + - - +
709A ARG* 3.2 12.3 - - - +
710A PRO* 3.7 26.2 - - + +
714A GLU* 2.8 41.4 + - - -
718A LYS* 4.6 9.1 - - - +
681D HIS* 4.5 30.0 + - + +
683D ARG* 5.6 6.3 - - - +
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Residues in contact with GLY 701 (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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648A VAL* 3.9 9.6 - - - -
649A PHE* 3.3 13.7 + - - -
652A ALA* 3.8 11.0 - - - -
697A LEU 2.7 23.9 + - - -
698A LEU 3.7 0.4 - - - -
700A ARG* 1.3 74.7 - - - +
702A TRP* 1.3 58.1 + - - +
703A ASN 3.4 0.2 - - - -
709A ARG* 3.2 21.8 - - - -
710A PRO* 3.9 14.3 - - - +
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Residues in contact with TRP 702 (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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649A PHE* 3.2 26.4 - - + -
652A ALA* 3.9 21.1 - - + -
653A LEU* 3.7 18.6 - - + -
656A TRP* 3.8 36.6 - + + -
683A ARG* 2.9 58.9 + - + +
684A PRO* 3.7 30.5 - - + -
686A ILE* 3.7 25.2 - - + +
698A LEU* 3.0 35.5 + - + -
699A ILE* 3.8 15.6 - - - +
701A GLY* 1.3 77.0 - - - +
703A ASN* 1.3 65.6 + - - +
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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