Contacts of the strand formed by residues 318 - 323 (chain E) in PDB entry 4CDC
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 318 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.6 6.1 - - - +
243E LEU* 3.8 15.8 - - - +
283E ALA 2.8 27.5 + - - -
284E GLY* 4.2 7.4 - - - -
287E ALA* 3.2 18.3 + - - +
288E GLN* 3.2 27.9 + - - +
317E TYR* 1.3 74.4 + - - +
319E SER* 1.3 60.1 + - - +
320E GLU 4.3 11.0 - - - -
321E TYR* 5.2 0.2 - - - -
433F ALA* 4.5 0.9 - - - -
434F THR 3.1 12.1 - - - -
435F PRO* 4.4 0.3 - - - +
436F ILE* 4.5 0.7 - - - -
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Residues in contact with SER 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 2.7 38.0 + - - -
105A VAL* 4.2 10.7 - - - +
106A LEU* 4.6 10.5 - - - +
288E GLN* 3.4 11.4 + - - +
318E SER* 1.3 72.3 - - - +
320E GLU* 1.3 64.3 + - - +
434F THR* 2.9 20.0 + - - +
436F ILE* 3.9 16.1 - - - +
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Residues in contact with GLU 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E GLN* 3.9 4.4 - - - +
318E SER* 3.3 3.2 + - - -
319E SER* 1.3 86.1 + - - +
321E TYR* 1.3 80.5 + - - +
322E HIS* 2.8 43.3 + - - +
432F ALA 4.4 1.6 - - - +
433F ALA* 3.3 1.9 - - - +
434F THR* 3.0 39.4 + - - +
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Residues in contact with TYR 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLU* 2.6 39.6 + - - -
76D LYS* 3.6 19.4 + - - +
280E TYR* 3.6 31.2 + + - -
284E GLY* 3.3 39.9 - - - -
285E LYS* 3.7 19.7 + - - +
288E GLN* 3.7 31.7 + - + -
289E ASP* 5.7 0.2 + - - -
318E SER* 5.2 1.3 - - - -
320E GLU* 1.3 85.2 - - - +
322E HIS* 1.3 67.7 + - - +
431F VAL* 5.4 2.7 - - + -
432F ALA 3.1 11.4 - - - +
433F ALA* 3.9 3.8 - - + -
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Residues in contact with HIS 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E TYR* 4.2 13.6 - - - -
320E GLU* 2.8 37.2 + - - +
321E TYR* 1.3 75.1 - - - +
323E TYR* 1.3 83.2 + - - +
324E VAL* 4.0 7.2 - - - -
325E GLY 4.9 0.7 - - - -
326E GLY* 4.8 11.2 - - - +
339E GLU* 4.0 12.9 + - - -
431F VAL* 3.5 2.2 - - - +
432F ALA* 2.7 55.9 + - + +
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Residues in contact with TYR 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D THR* 3.6 10.1 - - + -
62D ILE 3.7 19.3 - - - -
63D ILE* 3.5 30.1 - - + +
64D TYR 3.9 3.5 + - - -
278E PHE* 5.3 2.1 - - - +
280E TYR* 3.4 35.6 - + + +
322E HIS* 1.3 79.5 - - - +
324E VAL* 1.3 60.8 + - - +
325E GLY 3.2 0.2 + - - -
326E GLY* 2.8 25.8 + - - -
327E PHE* 3.6 22.1 - - - +
328E TYR* 3.3 24.5 - + + -
429F ILE* 3.6 29.5 - - + +
430F ALA 3.6 8.5 - - - +
431F VAL* 3.5 28.7 - - + -
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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