Contacts of the strand formed by residues 308 - 317 (chain E) in PDB entry 3QS7
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 THR 308 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275E VAL* 3.9 18.8 - - + -
276E HIS 3.2 22.4 - - - +
277E VAL* 3.4 11.0 - - + -
303E TYR* 3.2 10.4 - - - -
304E SER* 2.7 38.5 + - - +
305E THR* 2.7 26.6 + - - +
306E ASN* 3.0 7.8 + - - +
307E ARG* 1.3 75.4 - - - +
309E MET* 1.3 58.4 + - - +
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Residues in contact with MET 309 (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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9A SER 3.5 15.9 - - - +
11A ILE 4.7 0.2 - - - +
12A SER* 4.5 5.6 - - - +
275E VAL* 3.4 3.5 - - - +
276E HIS 2.8 33.3 + - - -
277E VAL 4.0 0.4 + - - -
278E ASN 3.9 3.1 - - - +
279E HIS* 3.8 32.1 - - + +
281E PHE* 3.8 9.3 - - + -
301E SER* 3.6 23.8 - - - +
302E THR 3.5 12.1 - - - +
303E TYR* 3.9 32.1 - - + +
308E THR* 1.3 72.6 - - - +
310E ILE* 1.3 67.0 + - - +
311E ARG* 3.5 39.7 - - - +
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Residues in contact with ILE 310 (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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225E PHE* 3.3 26.9 - - + -
226E GLY* 5.3 7.0 - - - +
273E LYS* 5.1 8.1 - - + -
274E ALA 3.6 5.8 - - - +
275E VAL* 3.9 32.5 - - + -
301E SER* 3.4 3.8 - - - -
302E THR* 2.9 57.9 + - + +
303E TYR 3.9 2.7 - - - +
304E SER* 3.5 27.1 - - - -
309E MET* 1.3 75.0 - - - +
311E ARG* 1.4 68.0 + - - +
312E ILE* 5.3 0.4 - - + -
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Residues in contact with ARG 311 (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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8A HIS* 3.5 11.7 - - - +
9A SER* 3.5 27.3 + - - +
272E CYS 3.4 1.7 - - - +
273E LYS* 3.3 6.6 - - - +
274E ALA 3.0 31.2 + - - -
279E HIS 2.7 29.0 + - - -
281E PHE* 2.8 45.0 + - + -
282E GLY* 4.6 4.8 - - - -
283E LEU* 3.8 23.3 - - + +
299E GLU* 6.3 3.4 - - - -
300E MET 3.7 3.4 - - - +
301E SER* 3.5 14.7 + - - -
309E MET* 3.5 25.5 - - - +
310E ILE* 1.4 76.1 - - - +
312E ILE* 1.3 62.3 + - - +
313E LEU* 4.1 3.6 - - + -
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Residues in contact with ILE 312 (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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224E LEU* 3.3 33.0 - - + +
225E PHE* 3.6 35.9 - - + -
226E GLY 4.8 1.3 - - - +
271E ARG* 4.3 15.7 - - + -
272E CYS 3.4 7.2 - - - +
273E LYS* 5.0 10.3 - - + -
298E PHE 3.6 1.2 - - - +
299E GLU* 3.2 4.6 - - - +
300E MET* 2.8 59.7 + - + +
310E ILE* 5.3 0.7 - - + -
311E ARG* 1.3 75.5 - - - +
313E LEU* 1.3 60.8 - - - +
314E PHE* 3.7 27.8 - - + +
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Residues in contact with LEU 313 (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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272E CYS* 3.0 21.8 + - + +
283E LEU* 3.5 57.9 - - + +
284E THR* 3.8 9.2 - - - +
285E TRP* 2.6 54.9 + - + +
297E TYR* 5.6 4.9 - - + -
298E PHE 3.4 8.3 - - - +
299E GLU* 3.7 23.6 - - + -
311E ARG* 4.1 3.7 - - + -
312E ILE* 1.3 69.9 - - - +
314E PHE* 1.3 56.0 + - - +
330E CYS* 5.3 1.1 - - - -
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Residues in contact with PHE 314 (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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175E LYS* 4.7 12.1 - - + -
181E ALA 6.0 4.9 - - - -
182E LEU* 5.4 2.2 - - + -
224E LEU* 4.6 11.7 - - + -
244E LEU* 6.3 0.7 - - + -
269E TRP* 3.6 36.6 - + + -
270E ILE 3.3 14.1 - - - +
271E ARG* 3.6 17.9 - - + +
285E TRP* 3.6 1.1 - - - -
297E TYR* 3.5 3.3 - - - +
298E PHE* 2.9 74.5 + + + -
300E MET* 3.5 27.1 - - + -
312E ILE* 3.7 16.4 - - + -
313E LEU* 1.3 75.5 - - - +
315E ALA* 1.3 62.3 + - - +
316E PHE* 4.9 5.2 - + - -
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Residues in contact with ALA 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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269E TRP* 3.7 3.1 - - - -
270E ILE* 2.8 49.6 + - + +
285E TRP* 3.3 33.1 - - + +
292E LEU* 4.0 11.9 - - + -
296E ASN 3.2 11.9 - - - +
314E PHE* 1.3 75.1 - - - +
316E PHE* 1.3 63.4 + - - +
328E TYR* 5.6 1.3 - - + -
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Residues in contact with PHE 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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175E LYS* 6.0 4.0 - - + -
268E LEU* 3.0 13.5 - - - +
269E TRP* 3.6 42.6 - + + -
295E GLY* 3.3 23.0 - - - +
296E ASN* 3.0 51.4 + - - +
297E TYR* 3.9 10.5 - - - -
298E PHE* 5.5 3.6 - - + -
314E PHE* 4.9 7.0 - + - -
315E ALA* 1.3 75.8 - - - +
317E VAL* 1.3 73.0 + - - +
318E SER* 4.2 14.6 - - - -
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Residues in contact with VAL 317 (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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267E PRO* 3.1 10.9 - - - +
268E LEU* 2.9 60.9 + - + +
269E TRP* 4.9 0.3 + - - -
296E ASN* 5.5 4.0 - - + -
316E PHE* 1.3 81.4 - - - +
318E SER* 1.4 61.8 + - - +
319E SER 3.5 22.4 - - - +
320E VAL* 3.7 10.3 - - + -
324E ASP* 3.5 26.9 - - - +
328E TYR* 4.5 7.2 - - + +
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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