Contacts of the strand formed by residues 680 - 685 (chain D) in PDB entry 2FGJ
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 LYS 680 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486D ASP* 3.3 41.9 + - + +
487D ASN* 4.4 13.7 - - - +
488D ILE* 4.1 5.6 - - - -
506D SER 4.5 0.4 + - - -
676D MET* 3.2 7.2 - - - -
677D GLU 3.0 33.1 + - - +
678D LYS* 4.3 12.1 - - + +
679D GLY* 1.3 84.0 - - - +
681D ILE* 1.3 66.8 + - - +
682D VAL* 3.4 7.2 + - + +
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Residues in contact with ILE 681 (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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488D ILE* 3.9 31.8 - - + +
489D ASN 3.9 23.8 - - - +
490D LEU* 4.5 15.3 - - + -
511D LEU* 5.3 1.8 - - + -
674D ILE* 3.8 25.6 - - + -
675D VAL 3.5 7.2 - - - +
676D MET* 4.3 6.5 - - - +
680D LYS* 1.3 73.7 - - - +
682D VAL* 1.3 62.4 + - - +
683D GLU 3.7 21.5 - - - +
684D GLN* 4.5 15.0 - - + +
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Residues in contact with VAL 682 (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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675D VAL* 2.9 22.9 + - + +
677D GLU* 4.2 23.1 - - + +
680D LYS* 3.9 14.1 - - + +
681D ILE* 1.3 76.7 - - - +
683D GLU* 1.3 75.1 + - + +
697D LEU* 4.0 27.1 - - + -
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Residues in contact with GLU 683 (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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674D ILE* 3.8 0.3 - - - -
675D VAL* 2.9 43.9 + - + +
681D ILE* 3.7 4.9 - - - +
682D VAL* 1.3 90.7 - - - +
684D GLN* 1.3 62.9 + - - +
690D LEU* 3.9 9.6 - - + -
696D SER* 3.3 17.6 - - - -
697D LEU* 2.9 30.8 + - - +
698D TYR* 2.9 31.6 + - - +
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Residues in contact with GLN 684 (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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489D ASN 4.9 5.9 - - - +
490D LEU* 4.5 6.1 - - - +
672D ARG* 3.8 35.5 + - + +
673D ILE 3.4 6.7 - - - +
674D ILE* 4.4 10.7 - - + +
681D ILE* 4.5 13.2 - - + +
683D GLU* 1.3 78.9 - - - +
685D GLY* 1.3 60.6 + - - +
689D GLU* 5.7 0.9 - - - +
690D LEU* 3.6 12.2 - - - +
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Residues in contact with GLY 685 (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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672D ARG* 4.3 9.6 - - - +
673D ILE* 2.9 32.6 + - - +
684D GLN* 1.3 80.4 - - - +
686D LYS* 1.3 68.1 + - - +
689D GLU* 4.0 9.6 - - - -
690D LEU* 3.5 10.9 - - - +
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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