Contacts of the strand formed by residues 279 - 288 (chain A) in PDB entry 3I7L
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 ARG 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ILE* 2.8 44.7 + - - +
255A GLN* 3.0 40.5 + - - +
256A SER* 4.0 7.1 - - - +
273A LEU 3.7 1.9 - - - +
274A GLY* 4.3 1.4 - - - -
275A ASP* 3.2 38.3 + - - +
277A GLU* 3.7 28.5 - - + +
278A GLY* 1.3 80.3 - - - +
280A LEU* 1.3 60.3 + - - +
281A PHE* 3.5 24.9 - - + -
304A LEU* 4.2 15.5 - - + +
306A GLY 3.2 11.7 - - - +
307A GLU* 4.4 7.9 - - + +
308A THR* 5.3 0.4 + - - -
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Residues in contact with LEU 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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272A LEU* 4.1 26.2 - - + -
273A LEU 3.3 25.1 - - - +
274A GLY* 4.9 0.9 - - - -
278A GLY 3.7 0.2 + - - -
279A ARG* 1.3 73.3 - - - +
281A PHE* 1.3 74.6 + - - +
304A LEU* 3.7 4.7 - - - +
305A LEU* 2.8 33.6 + - + +
306A GLY 2.8 16.0 + - - +
308A THR* 4.1 29.8 - - + +
314A LEU* 4.1 13.5 - - + -
322A VAL* 4.9 9.6 - - + -
334A VAL* 5.3 0.4 - - + -
336A LEU* 4.4 20.4 - - + -
347A VAL* 4.9 4.3 - - + -
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Residues in contact with PHE 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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252A ILE* 4.1 11.0 - - + -
253A ILE* 3.8 25.6 - - + -
258A ILE* 5.2 4.7 - - + -
272A LEU* 3.5 10.4 - - - +
273A LEU* 3.1 51.7 + - + -
275A ASP* 3.6 28.7 - - + -
279A ARG* 3.5 37.5 - - + -
280A LEU* 1.3 81.1 - - - +
282A MET* 1.3 62.0 + - - +
283A LEU 4.1 0.7 - - - -
302A VAL* 3.4 27.4 - - + -
303A GLU 3.2 4.3 - - - +
304A LEU* 3.7 28.7 - - + -
305A LEU* 4.2 3.6 - - - -
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Residues in contact with MET 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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264A VAL* 4.2 7.4 - - + -
270A ARG* 3.9 38.6 - - + +
271A TYR 3.2 21.1 - - - +
272A LEU* 3.9 13.9 - - + -
281A PHE* 1.3 75.1 - - - +
283A LEU* 1.3 62.6 + - - +
284A LEU* 3.8 29.2 + - + +
301A ARG 3.6 0.3 - - - +
302A VAL* 3.0 6.1 - - - -
303A GLU* 2.7 38.2 + - + +
305A LEU* 3.7 33.4 - - + +
336A LEU* 4.2 9.0 - - + -
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Residues in contact with LEU 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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220A ILE* 4.9 5.8 - - + -
230A ILE* 4.4 25.1 - - + -
232A ILE* 5.1 1.6 - - + -
237A ILE* 4.2 22.9 - - + -
248A ILE* 4.8 0.7 - - + -
269A SER 3.8 0.5 - - - +
270A ARG* 3.2 5.5 - - - +
271A TYR* 2.8 52.2 + - + +
273A LEU* 3.4 36.9 - - + +
281A PHE 4.1 0.6 - - - -
282A MET* 1.3 72.7 - - - +
284A LEU* 1.3 61.0 + - - +
285A LEU* 4.3 7.0 - - + -
300A LEU* 4.4 17.7 - - + -
301A ARG 3.2 17.0 - - - +
302A VAL* 4.3 12.1 - - + +
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Residues in contact with LEU 284 (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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269A SER 3.5 1.6 - - - +
270A ARG* 3.5 30.5 - - + -
282A MET* 3.8 20.9 - - + +
283A LEU* 1.3 75.9 - - - +
285A LEU* 1.3 65.6 + - - +
286A GLU* 3.6 3.6 + - - +
300A LEU* 3.4 5.0 - - - +
301A ARG* 2.6 72.0 + - + +
303A GLU* 3.3 35.2 - - + +
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Residues in contact with LEU 285 (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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222A VAL* 3.8 23.6 - - + -
226A PHE* 3.8 25.6 - - + -
230A ILE* 3.8 24.5 - - + -
239A TYR* 5.3 2.2 - - + -
268A GLY 2.9 23.3 - - - +
269A SER* 2.5 25.4 + - - +
271A TYR* 4.7 4.7 - - + -
283A LEU* 4.3 12.6 - - + +
284A LEU* 1.3 73.8 - - - +
286A GLU* 1.3 59.8 + - - +
287A LYS* 3.0 13.3 + - - +
297A LEU* 3.7 7.9 - - + -
300A LEU* 3.2 27.4 - - + -
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Residues in contact with GLU 286 (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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284A LEU 3.6 3.6 + - - +
285A LEU* 1.3 68.2 - - - +
287A LYS* 1.3 74.1 + - - +
297A LEU* 3.6 4.4 - - - -
298A LYS* 2.7 71.0 + - + +
299A ASP* 2.9 32.3 + - + +
301A ARG* 5.6 12.8 - - + +
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Residues in contact with LYS 287 (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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225A PRO* 5.6 2.5 - - - -
226A PHE* 3.6 31.9 - - + -
267A ASN* 3.8 30.5 + - - +
269A SER* 4.3 8.3 - - - -
285A LEU 3.0 6.5 + - - +
286A GLU* 1.3 87.0 + - - +
288A GLU* 1.3 67.7 + - - +
295A VAL* 4.7 23.6 - - + -
296A THR 3.5 9.0 - - - +
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Residues in contact with GLU 288 (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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287A LYS* 1.3 84.2 - - - +
289A GLU* 1.3 69.8 + - - +
290A GLN* 3.8 16.9 + - - +
295A VAL* 3.9 2.7 - - - -
296A THR* 3.1 58.6 + - + +
298A LYS* 4.0 31.5 - - + +
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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