Contacts of the strand formed by residues 32 - 41 (chain A) in PDB entry 1G13
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 ASN 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PRO* 3.7 18.4 - - - +
27A ILE* 4.7 3.1 - - - +
28A ILE* 4.4 2.6 + - - +
31A GLY* 1.3 80.8 + - - -
33A VAL* 1.3 62.4 + - - +
120A GLU* 4.3 22.6 - - + +
121A PHE 3.3 9.2 + - - +
122A VAL* 3.2 37.5 - - - +
123A VAL* 4.1 3.1 - - - +
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Residues in contact with VAL 33 (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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22A LEU* 3.2 40.4 - - + -
23A GLU 3.2 17.7 - - - +
27A ILE* 4.2 15.3 - - + -
32A ASN* 1.3 75.7 - - - +
34A THR* 1.3 62.4 + - - +
35A LEU* 3.9 1.3 + - + +
119A SER 3.5 1.4 - - - +
120A GLU* 3.5 2.8 - - - -
121A PHE* 2.9 54.6 + - + +
123A VAL* 4.2 17.7 - - + +
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.6 2.1 + - - +
22A LEU* 3.4 4.9 + - - -
23A GLU* 2.6 50.7 + - - +
24A PRO* 5.7 0.7 - - - +
33A VAL* 1.3 72.6 - - - +
35A LEU* 1.3 61.7 + - - +
118A LYS* 3.6 36.3 - - + -
119A SER 3.4 8.3 - - - +
120A GLU* 2.7 29.7 + - - +
79B HIS* 3.8 11.3 + - + +
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Residues in contact with LEU 35 (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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20A LEU* 3.3 34.3 - - + -
21A THR* 3.3 11.4 - - - +
22A LEU* 3.9 19.5 - - + -
33A VAL* 3.9 3.0 + - + +
34A THR* 1.3 75.0 - - - +
36A SER* 1.3 63.8 + - - +
37A VAL* 4.5 7.2 - - + -
116A LEU* 4.2 15.7 - - + +
117A PRO 3.7 2.4 - - - +
118A LYS* 3.3 2.1 - - - -
119A SER* 2.9 35.5 + - - +
121A PHE* 3.9 30.3 - - + -
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Residues in contact with SER 36 (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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19A SER* 5.4 1.7 + - - -
20A LEU* 3.4 5.0 - - - +
21A THR* 2.8 55.9 + - - +
35A LEU* 1.3 73.7 - - - +
37A VAL* 1.3 67.8 + - - +
116A LEU* 3.2 9.4 - - - -
118A LYS* 3.3 32.2 - - - +
82B ASP* 3.7 2.1 + - - -
86B MSE 3.6 15.4 - - - +
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Residues in contact with VAL 37 (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 ILE* 4.2 19.7 - - + -
19A SER* 3.3 15.9 - - - +
20A LEU* 3.8 16.2 - - + -
35A LEU* 4.5 8.7 - - + -
36A SER* 1.3 79.9 + - - +
38A MSE 1.3 72.3 + - - +
39A GLY 4.7 0.4 - - - +
114A TYR 4.0 0.5 - - - +
115A SER* 3.6 0.5 - - - -
116A LEU* 2.8 54.2 + - + +
86B MSE 4.3 2.5 - - - +
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Residues in contact with MSE 38 (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 ILE* 3.7 2.6 - - - +
18A ARG* 2.7 64.9 + - + +
19A SER* 2.9 31.6 + - - +
37A VAL* 1.3 78.9 - - - +
39A GLY* 1.3 53.5 + - - +
113A THR* 3.5 23.1 - - + -
114A TYR 3.2 7.6 - - - +
115A SER* 3.1 27.4 - - - +
86B MSE 4.4 12.3 - - - -
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Residues in contact with GLY 39 (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 VAL 3.1 14.4 - - - -
17A ILE* 4.0 8.5 - - - -
18A ARG* 3.9 3.8 - - - -
37A VAL* 4.7 1.2 - - - +
38A MSE 1.3 80.5 - - - +
40A SER* 1.3 62.8 + - - -
113A THR* 3.4 3.5 - - - +
114A TYR* 2.8 36.4 + - - +
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Residues in contact with SER 40 (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 PRO 3.6 1.1 + - - +
15A ALA* 3.4 2.1 - - - +
16A VAL* 2.8 40.8 + - - +
18A ARG* 3.2 39.2 + - - +
39A GLY* 1.3 76.6 - - - -
41A THR* 1.3 63.4 + - - +
112A GLY 3.2 15.3 - - - -
113A THR* 3.7 8.3 - - - -
114A TYR* 4.9 2.2 - - - -
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Residues in contact with THR 41 (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 PRO 3.1 8.8 + - - -
15A ALA* 4.0 12.4 - - - +
40A SER* 1.3 77.8 - - - +
42A SER* 1.3 58.0 + - - +
43A VAL* 2.5 36.9 + - - +
45A LEU* 3.5 28.8 - - + +
109A PHE 4.7 0.2 - - - +
110A LYS 3.9 19.3 - - - +
111A GLU* 3.3 4.0 - - - +
112A GLY 3.0 30.9 + - - +
114A TYR* 4.4 7.9 - - + -
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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