Contacts of the strand formed by residues 274 - 283 (chain A) in PDB entry 2QTL
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 PHE 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A PRO* 3.9 14.1 - - + -
273A VAL* 1.3 77.7 - - - +
275A GLN* 1.3 59.6 + - - +
276A VAL* 4.3 11.2 - - + -
303A THR* 3.7 20.6 - - + -
304A ASP* 3.1 28.7 - - - -
305A PHE* 3.6 43.5 - + + -
520A ILE 3.5 0.9 - - - +
521A SER* 3.3 3.0 - - - -
522A ILE* 2.7 54.3 + - + +
523A PHE* 4.5 0.2 - - - -
524A PRO* 3.7 20.4 - - + -
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 4.3 1.4 + - - +
274A PHE* 1.3 70.7 - - - +
276A VAL* 1.3 65.6 + - - +
277A PRO* 4.4 2.6 - - - +
303A THR* 4.8 5.4 - - - +
519A LYS* 3.7 31.3 - - + +
520A ILE 3.4 9.6 - - - +
521A SER* 4.3 13.3 + - - +
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A PHE* 4.3 9.6 - - + -
275A GLN* 1.3 79.9 - - - +
277A PRO* 1.3 67.9 - - - +
278A ILE 3.8 0.3 + - - -
298A LEU* 4.1 31.2 - - + -
299A ASP 3.5 21.1 - - - +
300A ILE* 4.1 11.9 - - + -
303A THR* 3.8 22.7 - - + -
305A PHE* 6.2 0.2 - - + -
519A LYS* 4.1 3.6 - - - -
520A ILE* 2.8 44.9 + - + +
522A ILE* 4.2 13.5 - - + -
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Residues in contact with PRO 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A GLN 4.4 2.7 - - - +
276A VAL* 1.3 85.7 - - - +
278A ILE* 1.3 62.4 + - - +
279A SER* 3.6 1.9 + - - -
298A LEU* 3.5 3.6 - - - -
299A ASP* 3.0 59.5 + - + +
517A ALA* 4.0 20.0 - - + -
518A PRO 3.3 7.9 - - - +
519A LYS* 3.9 11.9 - - + -
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A VAL 5.0 0.2 - - - +
277A PRO* 1.3 69.9 - - - +
279A SER* 1.3 58.5 + - - +
280A LYS 3.5 24.0 - - - +
296A VAL* 3.9 12.8 - - + -
297A GLU 3.5 6.7 - - - +
298A LEU* 3.7 19.5 - - + -
493A LEU* 4.8 6.1 - - + -
496A LEU* 3.9 12.8 - - + -
497A VAL* 3.8 30.7 - - + -
500A VAL* 4.1 14.3 - - + +
517A ALA* 3.4 19.4 - - - +
518A PRO* 2.8 30.1 + - + +
520A ILE* 3.9 25.6 - - + -
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PRO* 3.6 2.9 + - - -
278A ILE* 1.3 73.5 - - - +
280A LYS* 1.3 62.3 + - - +
297A GLU* 2.6 39.6 + - - +
299A ASP* 4.1 18.6 - - - +
465A LYS* 3.7 12.3 - - - +
500A VAL* 5.5 4.1 - - - +
517A ALA* 5.4 1.8 - - - -
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Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ILE* 3.5 10.0 - - - +
279A SER* 1.3 81.7 + - - +
281A ALA* 1.3 67.0 + - - +
282A VAL* 3.9 25.8 - - + +
295A LEU* 5.3 5.7 - - + +
297A GLU* 2.8 53.7 + - + +
467A HIS* 5.5 5.3 - - + +
500A VAL* 4.4 6.3 - - - -
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A LYS* 1.3 79.0 - - - +
282A VAL* 1.3 68.4 + - - +
294A LEU* 5.9 0.9 - - + -
295A LEU* 3.2 11.0 - - - +
296A VAL* 4.3 4.5 - - + -
497A VAL* 3.7 35.7 - - + -
500A VAL* 3.7 15.2 + - + +
501A LEU* 3.6 29.9 - - + +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A LYS* 3.9 31.4 - - + +
281A ALA* 1.3 80.9 - - - +
283A GLN* 1.3 74.4 + - - +
284A LEU* 3.5 13.5 + - + -
294A LEU* 3.4 3.3 - - - -
295A LEU* 2.8 54.1 + - + +
501A LEU* 3.9 4.9 - - - -
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A VAL* 1.3 77.6 - - - +
284A LEU* 1.3 62.1 + - - +
285A THR* 2.7 34.3 + - - +
286A THR* 3.7 8.3 + - - +
287A ASN* 3.1 29.0 + - - +
292A THR* 4.3 14.1 - - + +
293A THR 3.7 6.1 - - - +
294A LEU* 3.8 12.7 - - + +
501A LEU* 3.7 21.5 - - + +
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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