Contacts of the strand formed by residues 697 - 702 (chain D) in PDB entry 1FVU
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 GLU 697 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514B THR* 6.1 0.2 - - - +
301C LYS* 2.8 41.2 + - - -
670D ASP* 2.9 25.2 + - - +
671D VAL* 3.3 11.1 + - + +
672D TRP* 2.8 28.2 + - + -
695D GLU* 2.9 34.9 + - + +
696D TYR* 1.3 76.0 - - - +
698D CYS* 1.3 59.5 + - - +
710D ILE* 3.6 11.3 - - + +
711D ILE* 3.3 14.1 - - - +
712D PRO* 4.0 20.3 - - + +
713D CYS* 3.0 5.2 - - - -
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Residues in contact with CYS 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623D TRP* 3.4 35.7 - - + -
665D TRP* 3.6 13.0 - - + -
668D LEU 3.5 5.2 - - - +
669D SER* 3.4 21.5 - - - +
671D VAL* 5.0 0.2 - - - -
696D TYR* 4.4 0.4 - - - -
697D GLU* 1.3 72.9 - - - +
699D VAL* 1.3 65.5 + - - +
709D TRP 3.7 0.2 - - - +
710D ILE* 3.3 4.6 - - - -
711D ILE* 2.7 35.3 + - - +
713D CYS* 2.0 45.7 - - + -
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Residues in contact with VAL 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C GLN* 4.9 4.9 - - + -
295C VAL* 5.6 0.4 - - + -
665D TRP* 3.4 7.8 - - - -
666D ILE* 3.1 43.7 + - + +
668D LEU* 3.0 39.1 + - + -
671D VAL* 3.8 15.9 - - + -
698D CYS* 1.3 77.8 - - - +
700D ALA* 1.3 62.7 + - - +
708D TRP* 3.6 35.2 - - + -
709D TRP 3.5 6.7 - - - +
710D ILE* 4.2 14.4 - - + -
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Residues in contact with ALA 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663D VAL* 3.4 30.7 - - + -
664D VAL 3.0 17.9 - - - +
665D TRP* 3.8 17.0 - - + -
666D ILE* 4.3 0.9 - - - +
698D CYS 4.1 0.4 + - - -
699D VAL* 1.3 77.6 - - - +
701D SER* 1.3 59.1 + - - +
708D TRP* 3.5 1.6 - - - -
709D TRP* 2.8 37.2 + - + +
711D ILE* 4.2 5.2 - - + -
717D LYS* 5.1 0.2 - - + -
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Residues in contact with SER 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642D PHE* 4.0 12.4 - - - -
663D VAL* 4.0 2.5 - - - -
664D VAL* 2.7 45.2 + - - +
666D ILE* 3.9 20.7 - - - +
700D ALA* 1.3 73.9 - - - +
702D LYS* 1.3 61.5 + - - +
703D PRO* 3.2 3.6 - - - +
706D ASN* 3.5 29.1 + - - -
707D LYS 3.6 4.0 - - - -
708D TRP* 3.7 12.6 - - - -
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Residues in contact with LYS 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 3.7 26.2 - - + +
660D LYS* 5.3 1.5 - - - +
661D GLY* 3.8 29.4 - - - +
662D ASP 3.7 12.3 - - - +
663D VAL* 3.9 13.3 - - + +
700D ALA 4.2 0.2 + - - -
701D SER* 1.3 73.4 + - - +
703D PRO* 1.3 55.1 - - + +
704D THR* 2.8 44.7 + - + +
705D ASN* 3.5 7.8 + - - +
706D ASN* 2.8 22.0 + - - -
707D LYS 3.0 15.0 + - - +
709D TRP* 4.1 19.6 - - + +
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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