Contacts of the strand formed by residues 716 - 724 (chain A) in PDB entry 3FCS
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 716 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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713A ALA 3.6 15.9 - - - +
714A GLY 3.2 1.2 - - - -
715A GLU* 1.3 90.2 + - - +
717A VAL* 1.3 65.3 + - - +
718A SER* 5.4 1.6 + - - -
739A ASP* 4.7 15.2 + - - +
740A VAL 3.3 18.4 - - - -
741A PRO* 3.9 7.0 - - - -
742A VAL* 3.7 5.6 - - - -
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Residues in contact with VAL 717 (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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623A LEU* 3.5 30.3 - - + -
654A PRO* 4.3 15.7 - - + -
707A VAL* 5.2 7.4 - - + -
710A LEU* 4.6 9.4 - - + -
713A ALA* 3.7 29.8 - - + +
716A SER* 1.3 78.6 - - - +
718A SER* 1.3 61.9 + - - +
719A PHE* 4.1 18.7 + - + -
738A LEU 3.7 0.7 - - - +
739A ASP* 3.6 2.5 - - - -
740A VAL* 3.0 30.5 + - + +
742A VAL* 4.0 6.5 - - + +
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Residues in contact with SER 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A HIS 4.4 1.7 - - - +
653A LEU 4.9 0.2 - - - -
654A PRO* 3.9 21.1 - - - +
716A SER* 5.4 1.9 + - - -
717A VAL* 1.3 75.3 - - - +
719A PHE* 1.3 64.5 + - - +
720A GLN* 4.3 0.3 + - - +
737A LEU* 5.2 8.3 - - - -
738A LEU 3.5 4.0 - - - -
739A ASP* 3.6 21.3 + - - -
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Residues in contact with PHE 719 (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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618A VAL* 5.6 1.8 - - + -
631A LEU* 3.9 23.1 - - + -
633A LEU* 4.0 26.2 - - + -
651A VAL* 4.6 1.8 - - + -
652A HIS 3.9 8.1 - - - -
653A LEU* 4.0 12.8 - - + -
654A PRO* 3.4 33.7 - - + -
657A ALA* 4.0 15.0 - - + -
705A VAL* 4.1 8.7 - - + -
707A VAL* 4.0 12.6 - - + -
717A VAL* 4.1 13.9 - - + -
718A SER* 1.3 77.4 - - - +
720A GLN* 1.3 60.4 + - - +
721A LEU* 4.0 9.2 - - + -
737A LEU* 3.4 8.1 - - - +
738A LEU* 2.8 48.8 + - + +
740A VAL* 4.3 11.7 - - + -
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Residues in contact with GLN 720 (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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650A ALA 3.7 1.3 - - - +
651A VAL* 3.4 2.6 - - - +
652A HIS* 2.7 70.1 + - + +
718A SER 5.7 0.2 - - - +
719A PHE* 1.3 75.7 - - - +
721A LEU* 1.3 63.1 + - - +
722A GLN* 5.6 3.6 + - - +
735A ILE* 3.3 45.1 - - + +
736A VAL 3.5 3.1 - - - -
737A LEU* 3.4 17.8 - - + +
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Residues in contact with LEU 721 (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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614A LEU* 3.7 15.5 - - + +
616A ALA* 4.1 14.6 - - + -
633A LEU* 4.1 13.9 - - + -
635A MET* 3.2 35.2 - - + -
649A LEU* 4.5 4.3 - - + -
650A ALA 3.5 5.2 - - - +
651A VAL* 4.2 9.9 - - + -
652A HIS* 5.8 0.2 - - - -
719A PHE* 4.0 5.6 - - + +
720A GLN* 1.3 89.9 - - - +
722A GLN* 1.3 65.2 + - - +
735A ILE* 3.7 2.4 - - - +
736A VAL* 2.8 48.0 + - + +
738A LEU* 4.0 26.9 - - + -
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Residues in contact with GLN 722 (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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614A LEU* 3.7 7.1 - - - +
649A LEU* 3.3 6.5 - - - +
650A ALA* 2.7 47.0 + - + +
652A HIS* 5.7 5.1 - - + -
720A GLN* 5.6 3.5 + - + +
721A LEU* 1.3 78.0 - - - +
723A ILE* 1.3 66.3 + - - +
724A ARG* 4.1 18.8 + - + +
732A ASN* 3.5 22.4 + - - +
733A SER* 2.7 30.7 + - - +
734A LYS 4.0 2.9 - - - +
735A ILE* 3.6 27.8 - - + +
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Residues in contact with ILE 723 (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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612A LEU* 3.8 26.3 - - + +
613A GLN 3.3 21.5 - - - +
614A LEU* 4.0 15.9 - - + -
637A ALA* 3.3 30.7 - - + -
638A ALA 4.4 2.7 - - - +
647A ALA* 5.0 1.1 - - + -
648A GLU 3.5 6.7 - - - +
649A LEU* 4.4 4.3 - - + +
689A LEU* 3.5 27.4 - - + -
693A MET* 4.9 4.5 - - + -
722A GLN* 1.3 75.3 - - - +
724A ARG* 1.3 66.7 + - - +
732A ASN* 3.3 7.1 - - - +
733A SER* 2.9 43.5 + - - +
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Residues in contact with ARG 724 (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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646A GLU 3.6 1.8 - - - +
647A ALA* 3.4 3.8 - - - -
648A GLU* 2.8 51.0 + - + +
650A ALA* 3.7 24.1 - - + +
652A HIS* 3.6 28.7 + - - -
677A LYS* 5.9 1.0 - - - +
680A ASN* 4.3 15.8 + - - -
684A VAL* 5.3 0.4 - - - +
686A LEU* 4.3 17.8 - - - +
722A GLN* 4.1 19.5 + - - +
723A ILE* 1.3 81.0 - - - +
725A SER* 1.3 62.0 + - - +
731A PRO 4.1 0.4 - - - -
732A ASN* 3.5 14.6 - - - +
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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