Contacts of the strand formed by residues 348 - 354 (chain E) in PDB entry 6S7T
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 GLN 348 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C MET* 4.6 16.9 - - + +
343E TYR 4.3 0.2 - - - +
344E ASN* 3.5 1.2 - - - -
345E LEU* 2.9 37.8 + - + +
346E GLY 3.6 0.2 - - - -
347E ASP* 1.3 79.0 - - + +
349E TYR* 1.3 64.8 + - - +
427E HIS* 6.6 0.4 - - + -
428E TYR 3.5 6.1 - - - +
429E THR* 3.8 21.8 - - + +
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Residues in contact with TYR 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C MET* 5.0 1.5 - - - +
9C TYR* 4.2 9.7 + + - -
238E HIS* 3.3 44.4 - + - -
342E LEU* 4.5 7.4 - - + -
343E TYR 3.6 6.7 - - - +
344E ASN* 3.4 32.3 + - + -
346E GLY 4.2 9.0 - - - -
347E ASP 4.1 12.1 - - - -
348E GLN* 1.3 80.2 - - - +
350E ALA* 1.3 63.8 + - - +
426E VAL 4.5 0.2 - - - -
427E HIS* 3.4 5.0 + - - +
428E TYR* 2.9 54.3 + + + +
430E PHE* 3.9 22.7 + + + -
432E LYS* 3.2 35.0 + - - +
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Residues in contact with ALA 350 (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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3C LEU* 3.8 24.2 - - + -
6C MET* 3.9 12.8 - - + -
342E LEU* 3.4 5.2 - - - +
343E TYR* 2.9 35.6 + - - -
349E TYR* 1.3 78.0 - - - +
351E LEU* 1.3 61.4 + - - +
425E VAL* 5.6 0.9 - - + -
426E VAL 3.1 8.1 - - - +
427E HIS* 3.7 22.7 - - + +
428E TYR* 5.2 0.2 - - - -
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Residues in contact with LEU 351 (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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234E ILE* 4.9 3.4 - - + -
236E VAL* 3.5 37.5 - - + -
242E ILE* 4.9 8.7 - - + -
341E TYR 3.6 10.5 - - - +
342E LEU* 3.7 14.3 - - + +
350E ALA* 1.3 73.6 - - - +
352E LYS* 1.3 62.9 + - - +
353E MET* 3.8 37.5 - - + +
372E ILE* 4.9 13.7 - - + -
374E LEU* 5.3 0.2 - - + -
424E ILE* 4.8 3.6 - - + +
425E VAL* 3.0 6.1 - - - +
426E VAL* 2.9 52.8 + - + -
428E TYR* 4.7 3.5 - - + -
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Residues in contact with LYS 352 (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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3C LEU* 3.9 29.3 - - + +
341E TYR* 3.1 33.0 + - - +
343E TYR* 4.3 23.7 - - + +
350E ALA 4.1 0.4 + - - -
351E LEU* 1.3 71.6 - - - +
353E MET* 1.3 63.2 - - - +
423E ASP* 3.7 35.5 + - + +
424E ILE 3.4 3.6 - - - -
425E VAL* 3.7 20.8 - - + +
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Residues in contact with MET 353 (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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232E ARG* 4.5 10.8 - - - +
234E ILE* 3.8 31.6 - - + -
242E ILE* 3.7 24.9 - - + -
244E VAL* 3.8 23.3 - - + -
334E TYR* 5.8 1.1 - - - +
336E LEU* 4.7 12.1 - - + -
341E TYR* 4.1 22.2 - - + -
351E LEU* 3.8 21.6 - - + +
352E LYS* 1.3 78.5 - - - +
354E ARG* 1.3 68.9 + - + +
423E ASP* 3.0 13.5 - - - +
424E ILE* 2.9 35.4 + - + +
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Residues in contact with ARG 354 (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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232E ARG* 3.1 29.8 + - - +
234E ILE* 4.6 1.9 - - - +
283E ILE 5.4 0.6 + - - -
285E PRO* 5.6 4.5 - - - +
341E TYR* 5.8 3.2 - - + -
353E MET* 1.3 82.6 - - - +
355E PHE* 1.3 61.4 + - - +
356E VAL 4.2 11.0 - - - +
357E ASP* 3.0 30.9 + - + -
358E HIS 5.0 0.2 - - - +
370E VAL* 6.1 0.2 - - - +
421E ILE* 3.8 25.3 - - + +
422E GLN 3.2 8.7 - - - +
423E ASP* 3.3 15.7 + - - +
424E ILE* 5.0 3.1 - - - +
254I VAL* 2.7 42.2 + - - +
255I GLN 4.0 6.7 + - - -
256I SER* 3.9 22.1 + - - +
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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