Contacts of the strand formed by residues 314 - 318 (chain E) in PDB entry 6Q2J
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 TYR 314 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E ASP* 3.8 11.3 + - - -
302E ASP* 5.1 1.7 - - - +
303E VAL 5.3 0.5 + - - -
305E PRO* 3.3 45.4 + - + +
310E LEU* 3.0 45.1 + - + +
311E VAL* 4.1 6.9 - - - +
313E ARG* 1.3 81.7 - - - +
315E THR* 1.3 63.8 + - - +
316E SER* 3.7 2.1 + - - -
333E HIS* 4.2 24.0 - - + +
350E THR* 4.7 8.7 + - + +
352E HIS* 3.3 34.3 + + - -
354E TYR* 5.1 5.8 - - - +
376E VAL* 6.4 1.3 - - + -
377E ASN 3.3 3.6 - - - -
378E ASP* 3.2 37.5 - - + -
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Residues in contact with THR 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E VAL 4.4 12.3 - - - +
312E ARG 4.5 7.0 - - - +
313E ARG 4.6 2.0 - - - +
314E TYR* 1.3 78.7 - - - +
316E SER* 1.3 59.7 + - - +
317E THR* 4.0 9.9 + - - -
354E TYR* 5.5 1.1 - - - -
375E LEU 3.5 3.5 - - - +
376E VAL* 3.8 0.6 - - - -
377E ASN* 2.9 52.3 + - - +
703E NAG 3.7 28.1 + - + +
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Residues in contact with SER 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E TYR 3.7 3.0 + - - -
315E THR* 1.3 72.0 - - - +
317E THR* 1.3 61.8 + - - +
318E LEU 4.1 1.6 + - - -
331E VAL* 4.4 14.8 + - - +
333E HIS* 4.1 14.0 - - - +
354E TYR* 3.5 34.1 - - - -
374E VAL* 4.6 7.2 - - - -
375E LEU 3.2 8.3 - - - -
376E VAL* 4.8 0.2 - - - +
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Residues in contact with THR 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E THR* 4.6 11.8 + - - -
316E SER* 1.3 72.9 - - - +
318E LEU* 1.3 73.0 + - - +
319E LEU* 3.4 14.2 + - + -
320E PRO* 5.9 1.1 - - + -
331E VAL* 6.1 0.2 - - - -
374E VAL* 3.7 3.0 - - - -
375E LEU* 2.9 51.9 + - + +
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Residues in contact with LEU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E SER 4.1 2.4 + - - -
317E THR* 1.3 78.4 - - - +
319E LEU* 1.3 74.1 + - - +
320E PRO* 3.7 2.9 - - - +
325E ALA* 5.3 1.8 - - + +
326E GLN* 3.8 31.2 + - + +
329E PHE* 4.0 26.0 - - + +
330E ARG* 5.0 0.4 - - - -
331E VAL* 3.7 37.3 - - + +
356E LEU* 5.3 0.2 - - + -
372E LEU* 4.7 24.2 - - + -
373E ALA 3.9 12.1 - - - +
374E VAL* 4.0 7.6 - - + +
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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