Contacts of the strand formed by residues 684 - 690 (chain A) in PDB entry 1FCP
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 ASN 684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A ARG* 3.1 56.1 + - + +
673A TYR 3.3 19.1 - - - +
674A ASP* 4.3 2.2 - - - -
675A LEU* 3.9 8.9 - - - +
682A GLY 4.6 3.2 - - - +
683A SER* 1.3 80.1 - - - +
685A VAL* 1.3 71.5 + - - +
686A ALA* 3.9 5.1 - - - +
719A ALA* 3.7 1.7 - - - -
720A THR* 3.1 56.9 + - - +
721A PHE* 5.0 0.2 - - - -
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Residues in contact with VAL 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A VAL 4.2 0.5 - - - +
672A ARG* 3.8 0.5 - - - -
673A TYR* 3.1 34.2 + - + +
675A LEU* 3.8 26.7 - - + -
684A ASN* 1.3 79.7 + - - +
686A ALA* 1.3 70.0 + - - +
717A ALA* 6.4 1.3 - - + -
718A THR 3.3 7.9 - - - +
719A ALA* 4.6 14.1 - - + -
721A PHE* 5.2 1.3 - - + -
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Residues in contact with ALA 686 (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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670A LEU* 4.6 0.2 - - + -
671A VAL 3.4 10.5 - - - +
672A ARG* 3.9 18.2 - - + +
684A ASN* 3.9 6.0 - - - +
685A VAL* 1.3 82.3 - - - +
687A LEU* 1.3 61.6 + - - +
688A HIS* 3.5 24.9 - - + +
717A ALA* 3.4 5.7 - - - +
718A THR* 2.7 44.7 + - + +
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Residues in contact with LEU 687 (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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669A ALA 4.1 0.5 - - - +
670A LEU* 3.7 4.9 - - - +
671A VAL* 3.0 50.9 + - + +
686A ALA* 1.3 75.4 - - - +
688A HIS* 1.3 65.5 + - - +
689A VAL* 5.0 10.7 - - + +
715A VAL* 4.1 20.9 - - + -
716A VAL 3.4 15.3 - - - +
717A ALA* 4.3 12.3 - - + -
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Residues in contact with HIS 688 (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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59A ALA 4.4 2.5 - - - -
60A LEU* 2.8 35.1 + - - -
61A HIS* 3.9 12.6 - - - +
62A GLN* 3.1 39.2 + - + +
669A ALA 3.8 4.9 + - - +
670A LEU* 3.6 20.3 - - + +
672A ARG* 5.6 1.1 - - - -
686A ALA* 3.5 17.5 - - + +
687A LEU* 1.3 80.8 - - - +
689A VAL* 1.3 63.7 + - - +
690A ASN* 4.8 6.7 - - - +
714A GLN 3.6 1.0 - - - +
715A VAL* 3.4 3.6 - - - +
716A VAL* 2.9 45.2 + - + +
718A THR* 4.1 12.5 + - - -
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Residues in contact with VAL 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ASP* 3.5 5.2 - - - +
669A ALA* 3.2 38.9 + - + +
687A LEU* 5.0 13.0 - - + -
688A HIS* 1.3 81.1 - - - +
690A ASN* 1.3 69.0 + - - +
692A LEU* 3.6 45.8 - - + +
713A ARG* 4.0 12.6 - - + -
714A GLN 3.2 6.3 - - - +
715A VAL* 3.8 19.5 - - + -
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Residues in contact with ASN 690 (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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61A HIS* 4.6 23.5 + - - +
68A GLU* 6.2 1.8 - - - +
646A ARG* 4.6 8.4 - - - +
668A ASP* 3.1 25.5 + - - +
688A HIS* 4.8 5.9 - - - +
689A VAL* 1.3 79.7 + - - +
691A ASN* 1.3 75.1 + - + +
712A GLU 4.2 1.0 - - - +
713A ARG* 3.7 0.9 - - - +
714A GLN* 2.9 55.4 + - + +
716A VAL* 5.0 4.9 - - - +
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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