Contacts of the strand formed by residues 11 - 16 (chain f) in PDB entry 5GJQ
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 THR 11 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10f GLY* 1.3 72.6 - - - -
12f ILE* 1.3 73.6 + - - +
25f SER* 3.4 15.8 - - - -
26f ASP* 2.7 18.0 + - - +
42f LYS* 4.6 0.3 - - - +
138f GLY 3.7 6.5 - - - +
140f SER* 3.5 9.9 + - - -
141f ALA* 3.6 27.1 - - + +
145f LEU* 3.7 25.4 - - + -
179f PHE* 4.2 14.3 - - + -
182f ALA* 5.5 0.2 - - + -
189f THR* 2.4 30.2 + - + -
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Residues in contact with ILE 12 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11f THR* 1.3 85.8 - - - +
13f LEU* 1.3 68.5 + - - +
23f VAL* 5.0 4.7 - - + -
24f ALA 3.4 7.6 - - - +
25f SER* 3.9 6.3 - - - -
42f LYS* 3.7 17.5 - - + -
43f CYS* 5.5 0.4 - - - -
53f GLY* 3.5 9.9 - - - +
54f CYS 3.3 47.3 - - - +
55f SER* 3.6 12.8 - - - +
107f TYR 4.8 1.1 - - - +
109f ILE* 3.8 30.7 - - + -
137f ALA* 3.2 5.4 - - - +
138f GLY* 2.9 37.9 + - - +
179f PHE* 4.6 0.4 - - - -
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Residues in contact with LEU 13 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12f ILE* 1.3 77.8 - - - +
14f ALA* 1.3 78.0 + - - +
15f ILE* 4.7 1.6 - - + -
22f ILE* 4.5 0.6 - - - +
23f VAL* 3.5 3.1 - - - +
24f ALA* 2.9 31.9 + - + +
136f LYS 3.5 9.9 - - - +
137f ALA* 4.0 5.8 - - + -
145f LEU* 4.1 6.5 - - + -
149f LEU* 3.4 38.8 - - + -
175f VAL* 3.9 24.2 - - + -
178f VAL* 3.4 33.2 - - + -
179f PHE* 3.6 23.8 - - + -
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Residues in contact with ALA 14 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13f LEU* 1.3 81.5 - - - +
15f ILE* 1.3 64.3 + - - +
22f ILE* 3.0 16.4 - - - +
23f VAL* 4.3 9.2 - - + -
109f ILE* 3.7 28.0 - - + -
110f ILE 5.3 0.2 - - - +
121f VAL* 4.0 14.4 - - + +
135f PHE* 3.1 6.8 - - - +
136f LYS 2.9 32.5 + - - +
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Residues in contact with ILE 15 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13f LEU* 4.7 3.4 - - + -
14f ALA* 1.3 80.4 - - - +
16f ALA* 1.3 72.1 + - - +
17f GLY* 4.0 1.1 + - - -
20f PHE* 4.8 3.7 - - + -
21f ALA* 3.4 2.9 - - - -
22f ILE* 2.8 43.6 + - + +
121f VAL* 3.9 3.0 - - - +
134f SER 3.6 5.4 - - - +
135f PHE* 4.1 11.9 - - + -
149f LEU* 4.3 13.5 - - + -
153f VAL* 4.4 18.4 - - + -
171f ALA* 4.4 18.2 - - + +
174f LEU* 4.1 23.3 - - + -
175f VAL* 3.7 28.7 - - + -
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Residues in contact with ALA 16 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15f ILE* 1.3 81.0 - - - +
17f GLY* 1.3 60.3 + - - +
20f PHE 4.0 2.7 - - - -
21f ALA* 4.5 0.9 - - - +
119f GLY 3.9 26.0 - - - +
120f ALA* 4.0 1.6 - - - +
121f VAL* 3.8 19.1 - - + +
133f ASP 4.4 2.9 - - - +
134f SER* 2.7 30.1 + - - +
153f VAL* 6.0 1.0 - - - +
166f LEU* 5.7 2.1 - - - +
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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