Contacts of the strand formed by residues 328 - 331 (chain K) in PDB entry 3FKS
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 VAL 328 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169K ILE* 3.3 22.7 - - + +
177K LYS* 3.6 31.2 - - + +
181K ALA* 5.3 2.9 - - + -
269K VAL* 4.5 7.2 - - + -
270K TYR* 3.0 22.3 + - - +
271K ASP* 3.9 23.1 - - + +
272K ASP* 2.6 40.3 - - - +
273K LEU* 3.1 11.4 + - - +
326K LEU 4.0 5.8 - - - +
327K PRO* 1.3 80.2 - - - +
329K ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 329 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K LEU* 3.6 24.2 - - + +
169K ILE 3.0 7.5 + - - -
170K ILE* 3.4 14.4 - - + +
171K GLY 3.1 25.6 + - - +
177K LYS* 3.4 5.2 - - - +
272K ASP* 4.0 1.6 - - - -
273K LEU* 3.6 13.2 - - + -
274K SER* 3.1 35.0 - - - +
304K HIS* 5.8 0.2 - - - +
328K VAL* 1.3 75.9 - - - +
330K GLU* 1.3 63.6 + - - +
340K ILE* 4.4 4.9 - - + -
341K PRO* 4.0 32.5 - - + -
344K VAL* 3.7 28.7 - - + -
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Residues in contact with GLU 330 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K GLY 3.4 3.6 - - - -
173K ARG* 3.1 47.2 - - - +
177K LYS* 4.0 12.0 + - - +
272K ASP* 3.7 12.9 + - - +
274K SER* 2.9 21.8 + - - +
275K LYS* 2.9 27.9 + - - +
329K ILE* 1.3 73.2 - - - +
331K THR* 1.3 71.8 + - - +
332K GLN* 4.1 18.9 + - - +
341K PRO* 5.4 1.0 - - - +
323N ALA 5.6 1.0 - - - +
327N ALA* 5.3 4.2 - - - +
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Residues in contact with THR 331 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K ILE* 3.7 30.9 - - + +
171K GLY* 2.8 17.0 + - - -
172K ASP* 2.6 32.5 + - - +
173K ARG* 4.4 1.6 + - - +
330K GLU* 1.3 81.5 - - - +
332K GLN* 1.3 71.5 + - - +
333K GLY 4.2 0.3 + - - -
334K GLY* 4.1 2.6 - - - -
335K ASP 3.2 32.1 - - - +
336K VAL* 4.3 3.1 - - + -
341K PRO* 3.9 15.3 - - + -
353K PHE* 5.0 2.4 - - - -
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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