Contacts of the strand formed by residues 9 - 18 (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 ALA 9 (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* 1.3 77.0 - - - +
10A GLU* 1.3 62.6 + - - +
11A HIS* 5.7 2.5 - - + +
267A ARG* 4.5 1.3 - - - +
275A GLY 3.1 16.4 + - - +
276A VAL* 3.9 12.6 - - + -
277A VAL* 2.9 23.9 + - - +
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Residues in contact with GLU 10 (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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9A ALA* 1.3 78.0 - - - +
11A HIS* 1.3 75.0 + - - +
12A VAL* 3.9 13.2 - - + +
263A HIS* 2.7 44.4 + - + +
264A GLU* 4.7 3.1 - - - +
267A ARG* 3.4 34.4 + - - +
276A VAL* 4.3 0.4 - - - -
277A VAL 3.2 4.7 - - - -
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Residues in contact with HIS 11 (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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9A ALA* 5.7 2.7 - - + +
10A GLU* 1.3 83.4 - - - +
12A VAL* 1.3 61.3 + - - +
14A VAL* 3.5 21.1 - - + +
276A VAL* 3.8 18.9 - - + +
277A VAL 2.9 7.1 + - - +
278A ALA* 3.2 12.4 - - + +
279A SER 3.1 23.7 + - - -
309A LYS* 3.8 26.0 + - - -
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Residues in contact with VAL 12 (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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10A GLU* 3.9 16.6 - - + +
11A HIS* 1.3 76.2 - - - +
13A PRO* 1.3 73.6 + - + +
14A VAL* 4.3 0.2 - - - +
259A PHE* 3.6 28.0 - - + -
260A TYR* 3.7 20.6 + - + +
263A HIS* 3.7 36.6 - - + +
279A SER* 3.7 8.3 - - - +
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Residues in contact with PRO 13 (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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12A VAL* 1.3 87.5 + - + +
14A VAL* 1.3 63.0 + - - +
15A ILE* 4.1 16.2 + - + +
259A PHE* 3.5 31.0 - - + -
260A TYR* 3.9 14.6 - - + +
279A SER 3.6 5.4 - - - +
280A GLY* 5.0 0.2 - - - -
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Residues in contact with VAL 14 (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* 3.5 37.0 - - + +
12A VAL 4.3 0.2 - - - +
13A PRO* 1.3 76.4 - - - +
15A ILE* 1.3 63.9 + - - +
16A LEU* 4.0 23.3 - - + -
278A ALA* 4.3 9.2 - - + -
279A SER 2.8 14.4 + - - +
280A GLY* 3.2 21.1 - - - -
303A PHE* 3.2 19.0 - - + -
305A ARG* 6.0 1.6 - - - +
1010A ACY 5.4 2.7 - - - +
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Residues in contact with ILE 15 (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* 4.1 17.7 - - + +
14A VAL* 1.3 82.2 - - - +
16A LEU* 1.3 64.5 + - - +
17A GLU* 3.9 7.2 + - + +
259A PHE* 5.3 3.8 - - + -
280A GLY* 4.9 0.2 - - - -
281A GLU* 3.5 26.2 - - + +
283A VAL* 3.9 34.1 - - + -
297A VAL* 5.7 1.3 - - + -
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Residues in contact with LEU 16 (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* 4.0 17.0 - - + -
15A ILE* 1.3 73.9 - - - +
17A GLU* 1.3 59.4 + - - +
118A VAL* 4.0 15.9 - - + -
119A HIS* 3.7 27.4 - - + +
281A GLU 2.9 9.8 + - - +
282A LEU* 3.4 15.6 - - + +
283A VAL* 2.8 30.4 + - - +
303A PHE* 3.5 33.0 - - + -
305A ARG* 4.6 7.4 - - - +
1010A ACY 3.6 35.7 - - + +
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Residues in contact with GLU 17 (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 7.7 + - + +
16A LEU* 1.3 76.0 - - - +
18A SER* 1.3 72.3 + - - +
19A SER* 3.8 7.9 + - - +
118A VAL* 3.9 12.9 - - - +
283A VAL* 3.4 20.2 - - + +
285A ARG* 2.6 56.1 + - + +
297A VAL* 4.7 0.2 - - - +
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Residues in contact with SER 18 (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* 1.3 75.1 - - - +
19A SER* 1.3 63.2 + - - +
20A GLY* 3.5 11.3 + - - -
24A PHE* 5.8 2.1 - - - -
114A PRO 4.6 0.3 + - - -
115A GLU* 4.2 18.4 - - - -
117A ILE* 3.4 20.3 - - - +
118A VAL* 3.8 17.2 - - - +
283A VAL 2.9 13.1 + - - -
284A ILE* 3.3 8.6 - - - +
285A ARG 3.0 24.1 + - - -
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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