Contacts of the strand formed by residues 133 - 141 (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 CYS 133 (chain n).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30n VAL* 3.6 8.0 - - - +
77n VAL* 5.7 0.2 - - + -
78n ALA 3.3 14.4 - - - +
80n LEU 4.0 11.2 - - - +
83n ASP* 3.9 8.3 - - - -
84n ALA* 3.9 24.9 - - + +
87n LEU* 3.2 35.5 - - - +
131n PHE* 2.9 9.9 + - - +
132n GLY* 1.3 78.6 - - - +
134n SER* 1.3 63.8 + - - +
135n PHE* 4.6 7.3 - - - -
151n ILE 4.4 0.3 - - - +
152n ASP 4.2 1.6 - - - -
153n PRO* 3.3 18.4 - - - +
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Residues in contact with SER 134 (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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30n VAL* 3.5 22.4 - - - +
77n VAL* 3.6 1.0 - - - +
78n ALA 2.8 31.0 + - - -
133n CYS* 1.3 71.8 - - - +
135n PHE* 1.3 63.1 + - - +
150n MET* 4.4 2.0 - - - -
151n ILE 3.2 10.3 - - - -
152n ASP* 3.5 7.5 - - - +
153n PRO* 3.2 22.2 - - - +
165n ILE* 3.7 23.8 - - - +
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Residues in contact with PHE 135 (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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75n MET* 3.5 26.2 - - + -
76n ALA 3.2 11.2 - - - +
77n VAL* 3.6 17.3 - - + -
87n LEU* 3.6 29.4 - - + -
91n ALA* 6.1 1.1 - - + -
115n VAL* 3.4 31.6 - - + -
119n VAL* 4.5 1.1 - - + -
133n CYS* 4.6 5.2 - - - -
134n SER* 1.3 80.5 - - - +
136n MET* 1.3 64.6 + - - +
137n LEU* 4.0 19.1 - - + -
150n MET* 3.3 3.7 - - - +
151n ILE* 2.8 75.2 + - + +
165n ILE* 4.3 1.3 - - - -
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Residues in contact with MET 136 (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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36n ALA 4.3 5.2 - - - +
37n ILE* 4.0 7.6 - - - -
38n GLY* 3.5 38.8 - - - +
47n PHE* 3.7 21.5 - - + -
74n GLY 3.7 0.2 - - - +
75n MET* 3.1 9.7 - - - +
76n ALA* 2.7 46.3 + - + +
135n PHE* 1.3 77.3 - - - +
137n LEU* 1.3 61.9 + - - +
148n LEU* 4.0 9.6 - - + -
149n TYR 3.2 8.3 - - - +
150n MET* 4.1 9.0 - - + -
163n CYS* 3.6 28.5 - - + +
165n ILE* 3.9 19.5 - - + -
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Residues in contact with LEU 137 (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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69n VAL* 4.2 13.5 - - + -
73n VAL* 4.2 5.6 - - + -
74n GLY 3.2 4.0 - - - +
75n MET* 3.7 34.1 - - + -
91n ALA* 5.4 2.0 - - + -
108n LEU* 3.5 19.0 - - + +
111n LEU* 4.3 17.9 - - + +
112n ALA* 4.1 23.3 - - + +
115n VAL* 5.3 4.0 - - + -
135n PHE* 4.0 13.2 - - + -
136n MET* 1.3 74.4 - - - +
138n GLY* 1.3 59.9 + - - +
148n LEU* 3.3 6.5 - - - +
149n TYR* 2.9 35.6 + - + +
151n ILE* 4.1 20.9 - - + -
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Residues in contact with GLY 138 (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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45n VAL* 4.7 2.2 - - - -
47n PHE* 3.5 22.0 - - - -
73n VAL* 3.3 3.6 - - - +
74n GLY 2.9 33.5 + - - -
108n LEU* 4.1 1.1 - - - -
137n LEU* 1.3 74.7 - - - +
139n SER* 1.3 63.9 + - - -
147n GLN 3.4 7.0 - - - -
148n LEU* 4.2 2.2 - - - -
216n VAL* 4.1 9.9 - - - +
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Residues in contact with SER 139 (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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45n VAL* 3.9 4.6 - - - +
72n HIS* 2.9 33.1 + - - -
73n VAL* 4.0 0.9 - - - -
108n LEU* 3.6 32.5 + - - +
138n GLY* 1.3 76.3 - - - -
140n TYR* 1.3 70.1 + - - +
141n SER* 5.2 2.3 - - - -
145n GLY 4.0 0.8 - - - +
146n ALA* 3.6 1.2 - - - -
147n GLN* 2.9 32.6 + - - +
216n VAL* 3.9 9.8 - - - +
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Residues in contact with TYR 140 (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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42n LYS 4.8 3.4 - - - -
43n ASP* 4.3 7.6 - - - -
44n GLY* 4.0 13.7 - - - -
72n HIS* 4.0 5.7 + - - +
139n SER* 1.3 82.4 + - - +
141n SER* 1.3 77.9 - - - +
142n VAL* 4.6 16.8 - - + +
145n GLY* 3.5 10.8 - - - -
146n ALA* 3.7 25.6 - - + -
216n VAL* 3.6 11.6 - - + +
217n GLY* 3.5 23.6 - - - +
218n GLU* 3.5 42.9 + - + +
221n ASN 5.8 0.4 - - - -
222n GLY* 3.9 25.2 - - - +
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Residues in contact with SER 141 (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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72n HIS* 6.0 3.6 - - - -
139n SER* 5.2 3.1 - - - -
140n TYR* 1.3 86.7 - - - +
142n VAL* 1.3 65.7 + - - +
143n ASN* 3.2 17.0 + - - +
144n ASP* 3.7 13.6 + - - +
145n GLY* 2.9 33.8 + - - +
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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