Contacts of the strand formed by residues 276 - 285 (chain A) in PDB entry 2IGT
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 VAL 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PRO* 4.2 0.7 - - - -
9A ALA* 3.4 24.0 - - + +
11A HIS* 3.8 33.9 - - + +
274A GLY 3.9 0.8 + - - -
275A GLY* 1.3 75.5 - - - +
277A VAL* 1.3 74.4 + - - +
278A ALA* 4.2 2.2 + - + +
305A ARG 3.5 1.7 - - - +
306A TRP* 3.4 3.3 - - - +
307A GLU* 2.8 37.8 + - + +
309A LYS* 3.5 47.6 - - + +
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Residues in contact with VAL 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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8A PRO* 3.9 16.6 - - + -
9A ALA 2.9 8.1 + - - +
10A GLU* 3.2 4.7 - - - -
11A HIS 2.9 22.4 + - - -
263A HIS* 3.5 13.5 - - + +
266A MSE 3.6 24.9 - - + +
267A ARG* 3.9 20.4 - - + -
276A VAL* 1.3 76.3 - - - +
278A ALA* 1.3 61.1 + - - +
279A SER* 3.6 7.0 - - - +
304A SER* 3.3 26.9 - - - +
305A ARG 3.2 4.5 - - - +
306A TRP* 3.9 21.1 - - + -
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Residues in contact with ALA 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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11A HIS* 3.2 26.2 - - + +
14A VAL* 4.3 10.3 - - + -
276A VAL* 4.1 3.2 - - + -
277A VAL* 1.3 72.1 - - - +
279A SER* 1.3 61.8 + - - +
303A PHE* 3.5 10.0 - - + -
304A SER* 3.4 0.7 - - - -
305A ARG* 2.8 55.2 + - - +
307A GLU* 5.8 1.3 - - - +
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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
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11A HIS 3.1 6.9 + - - -
12A VAL* 3.7 6.6 - - - +
13A PRO* 3.6 7.3 - - - +
14A VAL* 2.8 27.8 + - - +
259A PHE 4.3 4.5 - - - -
263A HIS* 2.7 43.2 + - - +
277A VAL* 3.6 0.5 - - - +
278A ALA* 1.3 73.2 - - - +
280A GLY* 1.3 55.2 + - - +
303A PHE* 3.3 22.0 - - - -
304A SER* 2.8 23.5 + - - -
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Residues in contact with GLY 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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13A PRO* 4.8 0.2 - - - -
14A VAL 3.2 11.2 - - - -
15A ILE* 4.9 0.9 - - - -
259A PHE* 3.3 34.9 - - - +
279A SER* 1.3 76.6 - - - +
281A GLU* 1.3 59.8 - - - -
302A LEU* 3.4 2.1 - - - -
303A PHE* 3.0 35.2 + - - -
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Residues in contact with GLU 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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14A VAL 3.4 3.2 + - - -
15A ILE* 3.5 20.5 - - + +
16A LEU 2.9 26.0 + - - +
255A ILE* 6.5 0.4 - - - -
258A SER* 6.1 0.2 - - - -
259A PHE* 3.9 23.9 + - + -
280A GLY* 1.3 78.6 - - - +
282A LEU* 1.3 59.6 + - - +
283A VAL* 4.2 5.9 - - + +
299A SER* 2.7 36.5 + - - +
301A SER 3.4 4.0 - - - +
302A LEU* 4.0 18.3 - - + +
303A PHE* 3.6 5.7 - - - -
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Residues in contact with LEU 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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16A LEU* 3.4 23.6 - - + +
18A SER 5.1 0.2 - - - +
115A GLU* 3.5 43.5 - - + +
116A GLN* 3.5 30.5 - - - +
118A VAL* 3.9 21.3 - - + -
119A HIS* 4.0 16.6 - - + +
281A GLU* 1.3 70.7 - - - +
283A VAL* 1.3 67.4 + - - +
299A SER* 3.9 0.2 - - - -
300A THR* 2.9 34.4 + - - +
301A SER* 3.0 19.3 + - - +
303A PHE* 4.1 6.8 - - + -
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Residues in contact with VAL 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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15A ILE* 3.9 24.2 - - + -
16A LEU 2.8 16.0 + - - +
17A GLU* 3.4 24.8 - - + +
18A SER* 2.9 28.8 + - - -
281A GLU* 4.2 7.6 - - + +
282A LEU* 1.3 84.7 - - - +
284A ILE* 1.3 65.1 + - - +
297A VAL* 3.5 31.0 - - + -
298A LEU 3.4 7.0 - - - +
299A SER* 3.7 21.3 - - - +
300A THR 4.4 0.2 - - - +
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Residues in contact with ILE 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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18A SER* 3.3 11.7 - - - +
19A SER* 5.4 2.0 - - - -
24A PHE* 4.1 30.5 - - + -
26A LEU* 3.8 27.4 - - + +
34A LYS* 6.2 2.2 - - - +
36A GLU* 5.5 2.2 - - - +
114A PRO* 5.7 0.2 - - + -
115A GLU* 3.6 35.4 - - + +
283A VAL* 1.3 75.9 - - - +
285A ARG* 1.3 72.9 + - - +
286A GLU 4.0 0.2 + - - -
296A ARG 3.9 0.2 - - - +
297A VAL* 3.7 0.9 - - - -
298A LEU* 2.8 45.1 + - + +
300A THR* 3.6 21.1 - - + -
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Residues in contact with ARG 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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17A GLU* 2.6 46.7 + - - +
18A SER 3.0 7.7 + - - -
19A SER* 4.0 25.9 - - - +
26A LEU* 4.4 1.4 + - - +
283A VAL 4.4 0.2 + - - -
284A ILE* 1.3 83.0 - - - +
286A GLU* 1.3 76.7 + - - +
287A ALA* 3.4 1.4 + - - +
294A PRO* 3.8 25.6 - - - +
295A GLY 2.9 31.1 + - - +
296A ARG 3.5 4.9 - - - +
297A VAL* 3.4 28.9 - - + +
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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