Contacts of the strand formed by residues 145 - 151 (chain n) 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 GLY 145 (chain n).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139n SER 4.0 0.7 - - - +
140n TYR* 3.5 10.3 - - - -
141n SER* 2.9 38.6 + - - -
142n VAL 4.5 1.0 - - - -
143n ASN 3.9 0.2 - - - -
144n ASP* 1.3 82.4 - - - +
146n ALA* 1.3 61.6 + - - -
147n GLN* 3.9 3.6 + - - +
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Residues in contact with ALA 146 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40n ARG* 3.1 29.4 + - + +
41n CYS 4.3 11.0 - - - +
42n LYS 4.7 5.0 + - - +
44n GLY* 3.6 44.0 - - - +
45n VAL* 4.2 2.5 - - + -
139n SER 3.6 4.9 - - - -
140n TYR* 3.7 7.5 - - + -
144n ASP 5.2 0.3 - - - +
145n GLY* 1.3 72.7 - - - -
147n GLN* 1.3 65.1 + - - +
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Residues in contact with GLN 147 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65h THR* 5.4 2.9 - - - +
40n ARG* 4.4 11.7 + - - +
45n VAL* 3.6 4.5 - - - +
107n PRO* 6.2 0.2 - - - +
108n LEU* 3.3 35.2 - - + +
109n LYS* 4.0 13.6 - - - +
138n GLY* 3.4 1.9 - - - -
139n SER* 2.9 36.7 + - - +
144n ASP* 4.7 25.1 + - - +
145n GLY 3.9 6.0 + - - +
146n ALA* 1.3 80.5 - - - +
148n LEU* 1.3 63.8 + - - +
149n TYR* 3.8 23.2 + - + -
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Residues in contact with LEU 148 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38n GLY 3.6 32.3 - - - +
39n ILE* 4.0 7.2 - - - +
40n ARG* 4.3 14.6 + - + +
45n VAL* 4.2 8.3 - - + -
47n PHE* 3.5 29.2 - - + -
136n MET* 4.0 12.1 - - + -
137n LEU 3.3 15.7 - - - +
138n GLY* 4.2 1.1 - - - -
147n GLN* 1.3 78.6 - - - +
149n TYR* 1.3 73.4 + - - +
159n GLY* 3.3 5.4 - - - -
160n TYR* 2.9 53.5 + - + +
161n TRP 4.5 2.7 - - - +
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Residues in contact with TYR 149 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65h THR* 3.7 24.1 - - + +
108n LEU* 4.0 15.5 - - + -
109n LYS* 3.4 35.9 - - + +
112n ALA* 4.1 18.8 - - + -
136n MET* 3.2 6.6 - - - +
137n LEU* 2.9 38.0 + - + +
147n GLN* 3.8 25.6 + - + -
148n LEU* 1.3 82.4 - - - +
150n MET* 1.3 62.3 + - - +
151n ILE* 4.8 3.4 - - + -
157n SER* 3.6 21.5 - - - +
158n TYR* 3.1 22.9 - - - -
159n GLY* 3.9 10.8 - - - -
160n TYR* 4.7 1.3 - - - -
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Residues in contact with MET 150 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134n SER* 4.4 4.0 - - - -
135n PHE 3.3 10.8 - - - +
136n MET* 4.1 10.3 - - + -
149n TYR* 1.3 76.2 - - - +
151n ILE* 1.3 96.2 + - - +
152n ASP* 4.1 12.3 - - + +
156n VAL* 3.5 2.6 - - + +
157n SER* 3.1 5.7 - - - -
158n TYR* 2.9 30.1 + - + -
160n TYR* 3.6 37.5 - - + +
163n CYS* 3.5 24.9 - - + -
165n ILE* 4.2 20.2 - - + -
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Residues in contact with ILE 151 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112n ALA* 4.7 9.4 - - + +
115n VAL* 5.5 0.4 - - + -
116n ALA* 4.2 16.4 - - + +
119n VAL* 4.4 13.5 - - + -
133n CYS 4.4 0.2 - - - +
134n SER* 3.2 5.4 - - - -
135n PHE* 2.8 80.2 + - + +
137n LEU* 4.1 17.7 - - + -
149n TYR 4.8 1.1 - - - -
150n MET* 1.3 92.6 - - - +
152n ASP* 1.3 73.2 + - - +
155n GLY* 5.0 0.9 - - - -
156n VAL 3.2 9.6 - - - +
157n SER* 4.0 16.2 - - - +
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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