Contacts of the helix formed by residues 691 - 702 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560B LEU* 5.1 18.2 - - + -
659B LEU* 5.4 2.0 - - + -
688B TYR 4.8 1.5 - - - +
689B SER 4.0 5.6 - - - +
690B ILE* 1.3 89.7 - - + +
692B LYS* 1.3 58.4 + - - +
693B PRO* 3.3 8.7 - - + -
694B ILE* 3.0 44.2 + - + -
695B SER 3.0 11.5 + - - -
722B CYS* 6.4 0.4 - - - -
726B ILE* 5.8 2.7 - - + -
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Residues in contact with LYS 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690B ILE 3.9 1.2 + - - -
691B PRO* 1.3 71.0 - - - +
693B PRO* 1.3 71.4 - - + +
694B ILE 3.4 0.2 - - - -
695B SER* 3.4 20.7 + - - +
696B SER* 3.4 14.0 + - - -
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Residues in contact with PRO 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691B PRO* 3.4 11.9 - - + -
692B LYS* 1.3 95.8 - - + +
694B ILE* 1.3 61.9 + - + +
696B SER* 3.8 5.6 - - - -
697B LEU* 3.7 16.8 + - - +
718B LYS* 5.6 6.7 - - + +
722B CYS* 4.0 22.9 - - - -
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Residues in contact with ILE 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B LEU* 5.1 2.0 - - + -
564B LEU* 3.9 29.6 - - + -
655B LEU* 4.0 22.4 - - + -
659B LEU* 3.6 34.8 - - + -
690B ILE* 4.0 4.7 - - + -
691B PRO* 3.0 28.3 + - + +
693B PRO* 1.3 73.7 - - + +
695B SER* 1.3 59.2 + - - +
696B SER 3.0 2.2 - - - -
697B LEU* 2.6 33.0 + - - +
698B LEU* 3.0 12.0 + - + -
719B LEU* 4.3 9.0 - - + -
722B CYS* 4.1 20.2 - - + -
726B ILE* 5.8 1.1 - - + -
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Residues in contact with SER 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B ILE* 3.9 22.0 - - - +
690B ILE* 3.6 25.9 - - - +
691B PRO 3.0 9.6 + - - -
692B LYS* 3.4 17.3 + - - +
694B ILE* 1.3 76.5 - - - +
696B SER* 1.3 58.5 + - - +
698B LEU* 3.4 8.9 + - - +
699B ILE* 3.2 36.2 + - - +
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Residues in contact with SER 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692B LYS 3.4 15.4 + - - -
693B PRO* 3.8 6.5 - - - -
694B ILE 2.8 1.6 + - - -
695B SER* 1.3 80.1 + - - +
697B LEU* 1.3 62.5 + - - -
699B ILE* 3.4 7.1 + - - +
700B ARG* 3.1 33.6 + - - +
717C MET* 3.0 32.7 - - - +
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Residues in contact with LEU 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652B ALA* 5.2 0.3 - - - +
655B LEU* 4.9 10.3 - - + -
693B PRO 3.7 9.8 + - - +
694B ILE* 2.6 17.3 + - - +
696B SER* 1.3 72.2 - - - +
698B LEU* 1.3 58.5 + - - +
700B ARG* 3.8 24.1 - - - +
701B GLY* 2.8 28.9 + - - -
710B PRO* 4.4 17.6 - - + +
714B GLU* 4.7 2.7 - - - +
715B VAL* 4.2 31.0 - - + +
718B LYS* 4.0 34.3 - - + -
719B LEU* 4.2 18.4 - - + -
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Residues in contact with LEU 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652B ALA* 3.1 33.3 - - - +
655B LEU* 3.7 20.9 - - + -
656B TRP* 3.5 28.5 - - + +
659B LEU* 5.0 0.7 - - + -
686B ILE* 4.6 4.9 - - + -
690B ILE* 3.8 39.5 - - + -
694B ILE* 3.0 14.7 + - + +
695B SER* 3.5 9.4 - - - +
697B LEU* 1.3 75.8 - - - +
699B ILE* 1.3 58.1 + - - +
701B GLY* 3.3 0.9 + - - -
702B TRP* 3.0 51.9 + - + -
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Residues in contact with ILE 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B ILE* 3.7 23.3 - - + -
695B SER* 3.2 24.3 + - - +
696B SER* 3.8 8.5 - - - +
697B LEU 3.3 0.4 - - - -
698B LEU* 1.3 79.8 - - - +
700B ARG* 1.3 62.0 + - - +
702B TRP* 3.6 14.8 - - + +
703B ASN* 3.3 19.4 + - - +
713C SER* 5.5 3.1 - - - +
714C GLU* 3.7 55.2 - - + +
717C MET* 4.0 18.4 - - + -
718C LYS* 4.0 19.5 + - - +
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Residues in contact with ARG 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696B SER* 3.1 18.1 + - - +
697B LEU* 3.8 19.5 - - - +
699B ILE* 1.3 74.1 - - + +
701B GLY* 1.3 64.4 + - - +
703B ASN* 3.2 25.2 + - - +
708B GLY 4.2 11.1 + - - +
709B ARG* 3.3 13.2 - - - +
710B PRO* 3.7 23.5 - - + +
714B GLU* 2.7 43.4 + - - -
718B LYS* 4.9 4.9 - - - +
717C MET* 3.6 28.0 - - + -
718C LYS* 5.3 4.3 - - - +
721C GLU* 4.5 9.6 - - - +
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Residues in contact with GLY 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B VAL* 3.7 8.1 - - - +
649B PHE* 3.4 12.3 - - - -
652B ALA* 3.8 13.5 - - - -
697B LEU 2.8 23.3 + - - -
698B LEU 3.3 2.2 + - - -
700B ARG* 1.3 72.9 - - - +
702B TRP* 1.3 56.6 + - - +
709B ARG* 3.2 21.8 - - - +
710B PRO* 3.6 14.9 - - - +
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Residues in contact with TRP 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B PHE* 3.4 25.5 - - + -
652B ALA* 3.9 24.7 - - + -
653B LEU* 4.0 18.4 - - + -
656B TRP* 3.8 40.6 - + + -
683B ARG* 2.9 55.0 + - + +
684B PRO* 3.9 31.6 - - + -
686B ILE* 4.1 12.8 - - + +
698B LEU* 3.0 39.5 + - + -
699B ILE* 3.6 19.5 - - + +
701B GLY* 1.3 74.7 - - - +
703B ASN* 1.3 66.7 + - - +
714C GLU* 5.8 2.2 + - - -
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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