Contacts of the strand formed by residues 3 - 8 (chain b) 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 ILE 3 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1b THR* 4.1 13.7 - - + -
2b THR* 1.3 80.2 - - - +
4b ALA* 1.3 60.3 + - - +
15b GLY 3.3 7.6 - - - +
16b ALA* 3.9 16.8 - - + -
33b LYS* 4.6 4.0 - - + -
44b CYS* 3.7 32.5 - - + +
45b GLY 4.2 6.7 - - - +
46b ALA* 3.7 24.7 - - + +
97b ALA 4.5 1.3 - - - +
99b VAL* 3.9 10.5 - - + +
126b THR* 3.2 5.9 - - - -
127b MET* 3.0 51.8 + - + +
159b ILE* 4.0 0.4 - - - -
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Residues in contact with ALA 4 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3b ILE* 1.3 75.6 - - - +
5b GLY* 1.3 58.0 + - - +
13b VAL 4.5 0.4 - - - -
14b LEU* 3.5 3.6 - - - +
15b GLY 2.8 33.2 + - - +
44b CYS* 4.6 0.9 - - - -
99b VAL* 5.1 3.8 - - - -
125b VAL 3.3 7.9 - - - +
126b THR* 4.4 5.6 - - + -
134b ALA* 4.7 2.0 - - + -
138b PHE* 3.8 23.3 - - + -
155b VAL* 4.6 5.6 - - + -
158b ALA* 4.6 6.7 - - + -
159b ILE* 3.5 21.9 - - + +
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Residues in contact with GLY 5 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4b ALA* 1.3 77.6 - - - +
6b VAL* 1.3 61.9 + - - +
13b VAL 3.3 8.5 - - - -
14b LEU* 3.8 15.0 - - - -
99b VAL* 4.5 0.2 - - - -
110b LEU* 3.5 10.8 - - - -
124b TYR* 3.2 4.3 - - - +
125b VAL* 2.8 35.9 + - - +
138b PHE* 3.9 3.6 - - - -
155b VAL* 4.9 0.6 - - - +
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Residues in contact with VAL 6 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5b GLY* 1.3 72.9 - - - +
7b VAL* 1.3 71.1 + - - +
8b TYR 4.7 0.7 - - - +
12b ILE* 3.3 8.8 - - - +
13b VAL* 2.9 43.9 + - + +
110b LEU* 3.7 3.2 - - - +
123b PRO 3.4 11.0 - - - +
124b TYR* 3.9 7.9 - - + -
138b PHE* 4.7 3.1 - - + -
142b PHE* 3.7 29.6 - - + -
146b MET* 4.2 7.2 - - + -
151b ALA* 4.1 18.2 - - + +
154b LEU* 4.5 6.5 - - + -
155b VAL* 3.7 24.9 - - + -
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Residues in contact with VAL 7 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6b VAL* 1.3 80.5 - - - +
8b TYR* 1.3 69.5 + - - +
11b GLY 3.6 7.0 - - - +
12b ILE* 4.3 8.1 - - + -
108b PRO* 4.2 19.3 - - + +
109b HIS* 5.0 2.2 - - - -
110b LEU* 3.7 31.4 - - + +
122b LEU 4.2 0.4 - - - +
123b PRO* 2.8 33.5 + - + +
142b PHE* 4.3 11.4 - - - -
145b ASP* 4.7 11.4 + - - +
146b MET* 5.1 1.4 - - - +
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Residues in contact with TYR 8 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6b VAL 4.8 0.2 - - - -
7b VAL* 1.3 82.5 - - - +
9b LYS* 1.3 76.3 + - - +
10b ASP* 3.4 23.2 - - + +
11b GLY 2.8 37.3 + - - +
12b ILE* 3.2 22.9 - - - -
13b VAL* 3.8 28.5 - - + -
108b PRO* 4.3 4.0 - - - +
145b ASP* 4.3 6.8 - - - +
146b MET* 3.6 24.5 - - + +
147b GLU* 4.5 0.4 - - - -
148b GLU* 3.6 39.9 + - + -
151b ALA* 3.9 19.7 - - + -
177b VAL* 3.5 18.9 - - + +
178b ILE 4.4 0.2 + - - -
179b SER* 3.7 17.3 - - - -
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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