Contacts of the strand formed by residues 297 - 307 (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 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE* 5.7 1.3 - - + -
17A GLU* 4.7 3.8 - - - +
52A TRP* 3.6 20.3 - - - -
283A VAL* 3.5 36.3 - - + -
284A ILE 3.7 4.0 - - - -
285A ARG* 3.4 39.3 - - + +
296A ARG* 1.3 72.7 - - - +
298A LEU* 1.3 62.3 + - - +
299A SER* 4.1 4.2 + - - +
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Residues in contact with LEU 298 (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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26A LEU* 4.1 24.7 - - + -
29A SER* 5.5 2.7 - - - +
34A LYS* 4.1 18.6 - - + +
47A GLU* 3.7 44.0 - - + +
49A GLN* 3.9 23.1 - - + +
50A ALA* 5.0 0.2 - - + -
52A TRP* 4.4 18.8 - - + -
283A VAL* 3.4 1.7 - - - -
284A ILE* 2.8 51.7 + - + +
296A ARG 3.9 1.0 + - - -
297A VAL* 1.3 71.8 - - - +
299A SER* 1.3 64.0 + - - +
300A THR* 3.5 8.1 + - + +
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Residues in contact with SER 299 (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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49A GLN* 2.7 38.4 + - - +
255A ILE* 4.1 6.3 - - - +
281A GLU* 2.7 40.9 + - - +
282A LEU 4.0 0.2 + - - -
283A VAL* 3.7 17.1 - - - +
297A VAL* 3.9 6.1 + - - -
298A LEU* 1.3 75.3 - - - +
300A THR* 1.3 60.3 + - - +
301A SER 4.3 3.5 + - - -
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Residues in contact with THR 300 (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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115A GLU* 3.3 30.7 + - + +
253A TYR* 3.4 19.1 - - - +
255A ILE* 4.5 13.1 - - - +
282A LEU 2.9 15.9 + - - +
284A ILE* 3.6 31.2 - - + +
298A LEU* 3.6 20.0 - - + +
299A SER* 1.3 76.1 + - - +
301A SER* 1.3 77.1 + - - +
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Residues in contact with SER 301 (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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116A GLN* 3.9 6.2 + - - -
252A ALA 3.4 14.1 - - - -
253A TYR* 3.8 22.6 - - - +
255A ILE* 4.9 5.2 - - - +
281A GLU* 3.4 9.4 - - - +
282A LEU* 3.0 41.3 + - - +
299A SER* 3.8 2.8 + - - -
300A THR* 1.3 93.4 + - - +
302A LEU* 1.3 71.8 + - - +
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Residues in contact with LEU 302 (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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251A THR* 3.4 5.4 - - - +
252A ALA* 2.8 42.0 + - + +
254A SER* 3.8 17.3 - - - +
255A ILE* 4.7 13.0 - - + +
257A ALA* 3.8 27.6 - - + +
258A SER 3.9 8.1 - - - +
259A PHE* 3.8 17.3 - - - +
262A MSE 3.8 29.8 - - + -
280A GLY 3.4 6.5 - - - +
281A GLU* 4.0 23.1 - - + +
282A LEU* 5.6 0.2 - - - -
301A SER* 1.3 82.7 + - - +
303A PHE* 1.3 65.3 + - - +
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Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.2 35.4 - - + -
16A LEU* 3.5 31.2 - - + -
119A HIS* 3.6 33.2 - + + +
250A LEU* 3.1 13.2 - - - +
251A THR* 4.4 0.4 - - + -
259A PHE* 4.7 1.9 - - - +
262A MSE 4.9 4.9 - - - +
278A ALA* 3.5 26.7 - - + -
279A SER* 3.3 8.3 - - - -
280A GLY 3.0 52.3 + - - +
281A GLU 3.6 15.9 - - - -
282A LEU* 4.1 2.9 - - + -
302A LEU* 1.3 77.9 - - - +
304A SER* 1.3 66.4 + - - +
305A ARG* 4.3 11.9 - - + -
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Residues in contact with SER 304 (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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249A VAL* 3.7 0.8 - - - +
250A LEU* 2.9 36.8 + - - +
262A MSE 3.9 23.2 + - - -
263A HIS* 3.9 0.2 - - - -
266A MSE 3.3 33.5 - - - +
277A VAL* 3.3 5.7 - - - +
278A ALA 3.4 5.6 - - - -
279A SER* 2.8 20.2 + - - -
303A PHE* 1.3 76.4 - - - +
305A ARG* 1.3 59.1 + - - +
306A TRP 4.3 0.2 - - - -
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Residues in contact with ARG 305 (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* 6.0 1.6 - - - +
16A LEU* 4.6 6.3 - - - +
119A HIS* 4.6 14.2 + - - -
122A TRP* 3.9 37.8 - - + +
248A LEU 3.4 3.1 - - - +
249A VAL* 3.8 26.5 - - + +
276A VAL 3.5 2.3 - - - +
277A VAL* 3.2 5.7 - - - -
278A ALA* 2.8 56.9 + - - +
303A PHE* 4.6 11.3 - - + -
304A SER* 1.3 74.6 + - - +
306A TRP* 1.3 67.8 + - - +
307A GLU* 3.2 26.0 + - + +
309A LYS* 5.8 2.0 - - - +
1010A ACY 3.1 40.2 + - - -
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Residues in contact with TRP 306 (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* 4.2 1.6 - - + -
241A LEU* 4.4 7.9 - - + -
245A ALA* 4.3 24.5 - - + -
247A GLY* 3.2 9.4 - - - -
248A LEU* 2.9 44.8 + - + +
266A MSE 4.2 9.2 - - - +
270A MSE 3.5 56.3 - - + +
273A ALA* 4.0 17.9 - - + -
274A GLY 2.9 22.7 + - - -
276A VAL 3.4 12.3 - - - -
277A VAL* 3.9 14.4 - - + -
304A SER 4.3 0.2 - - - -
305A ARG* 1.3 74.4 - - - +
307A GLU* 1.3 71.9 + - - +
308A PRO* 3.8 37.0 - - + -
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Residues in contact with GLU 307 (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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122A TRP* 2.8 31.9 + - + -
246A LEU 3.7 11.2 - - - +
275A GLY* 3.2 1.0 - - - -
276A VAL* 2.8 34.3 + - + +
278A ALA* 5.8 1.4 - - - +
305A ARG* 3.2 32.0 + - + +
306A TRP* 1.3 85.9 - - - +
308A PRO* 1.4 69.7 - - + +
309A LYS* 3.0 44.8 + - + +
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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