Contacts of the strand formed by residues 32 - 41 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C PRO* 3.5 19.6 - - - +
27C ILE* 5.3 1.4 - - - +
28C ILE 5.0 3.1 + - - +
31C GLY* 1.3 83.9 + - - -
33C VAL* 1.3 62.7 + - - +
120C GLU* 4.6 20.8 - - - +
121C PHE 3.2 9.4 - - - +
122C VAL* 3.4 31.9 - - - +
123C VAL* 4.8 1.5 - - - +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 3.1 38.4 - - + -
23C GLU 3.2 13.2 - - - +
24C PRO* 4.4 0.2 - - - -
27C ILE* 4.9 11.0 - - + -
32C ASN* 1.3 75.1 - - - +
34C THR* 1.3 65.9 + - - +
35C LEU* 4.5 1.3 - - + +
119C SER 3.6 1.0 - - - +
120C GLU* 3.3 3.3 - - - -
121C PHE* 2.7 64.2 + - + +
122C VAL 5.0 0.2 - - - -
123C VAL* 4.4 19.1 - - + +
124C PRO* 6.1 0.9 - - + -
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Residues in contact with THR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A HIS* 4.0 14.8 + - + +
21C THR* 3.7 1.4 + - - +
22C LEU* 3.4 5.4 + - - -
23C GLU* 2.8 61.5 + - - +
24C PRO* 4.9 0.2 - - - +
33C VAL* 1.3 73.6 - - - +
35C LEU* 1.3 62.1 + - - +
118C LYS* 3.9 30.1 - - + -
119C SER 3.5 8.3 - - - +
120C GLU* 4.0 16.8 + - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU* 3.7 30.3 - - + -
21C THR* 3.3 10.3 - - - +
22C LEU* 4.1 19.7 - - + -
33C VAL* 4.0 1.7 + - + -
34C THR* 1.3 75.4 - - - +
36C SER* 1.3 63.9 + - - +
37C VAL* 4.8 6.5 - - + -
116C LEU* 4.2 16.2 - - + +
117C PRO 3.9 2.3 - - - +
118C LYS* 3.4 1.5 - - - -
119C SER* 3.0 32.2 + - - +
121C PHE* 3.6 32.3 - - + -
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Residues in contact with SER 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ASP* 3.8 7.2 + - - -
86A MSE 3.9 8.8 - - - +
19C SER* 5.3 1.2 + - - -
20C LEU* 3.2 5.1 - - - +
21C THR* 2.6 54.9 + - - +
35C LEU* 1.3 75.6 - - - +
37C VAL* 1.3 64.2 + - - +
116C LEU* 3.2 14.6 - - - -
118C LYS* 3.5 25.3 - - - +
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A MSE 4.1 2.8 - - - +
17C ILE* 4.0 27.4 - - + -
19C SER* 3.3 13.2 - - - +
20C LEU* 3.7 18.8 - - + -
35C LEU* 4.8 7.6 - - + -
36C SER* 1.3 76.8 - - - +
38C MSE 1.3 64.7 + - - +
39C GLY 4.8 0.2 - - - +
114C TYR 3.9 1.3 - - - +
115C SER* 3.7 0.5 - - - -
116C LEU* 2.8 52.8 + - + +
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Residues in contact with MSE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A MSE 4.4 11.0 - - + -
17C ILE* 3.6 2.3 - - - +
18C ARG* 2.7 63.9 + - + -
19C SER* 2.9 30.6 + - - +
37C VAL* 1.3 79.4 - - - +
39C GLY* 1.3 68.7 + - - +
40C SER* 5.4 0.7 - - - -
113C THR* 3.5 23.6 - - + -
114C TYR 3.3 3.8 - - - +
115C SER* 3.3 22.9 - - - +
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Residues in contact with GLY 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL 3.3 13.2 - - - -
17C ILE* 4.0 8.5 - - - -
18C ARG* 3.9 4.5 - - - -
37C VAL* 4.8 0.8 - - - +
38C MSE 1.3 81.5 - - - +
40C SER* 1.3 65.5 + - - -
113C THR* 3.4 4.5 - - - +
114C TYR* 2.8 35.2 + - - +
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PRO 3.3 2.4 - - - +
15C ALA* 4.4 0.4 - - - -
16C VAL* 3.0 35.2 + - - +
18C ARG* 4.0 23.1 + - - +
38C MSE 5.4 0.2 - - - -
39C GLY* 1.3 75.7 - - - -
41C THR* 1.3 60.9 + - - +
112C GLY 3.1 18.6 - - - -
113C THR* 3.7 15.3 - - - -
114C TYR* 4.7 3.1 - - - +
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Residues in contact with THR 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PRO 2.9 7.9 + - - -
15C ALA* 3.8 14.4 - - - +
40C SER* 1.3 76.8 - - - +
42C SER* 1.3 59.6 + - - +
43C VAL* 2.7 36.2 + - - +
45C LEU* 3.6 25.9 - - + +
109C PHE 5.4 0.2 - - - -
110C LYS 3.9 19.3 - - - +
111C GLU* 3.3 2.7 - - - +
112C GLY 3.0 30.3 + - - +
114C TYR* 4.4 8.5 - - + -
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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