Contacts of the strand formed by residues 129 - 136 (chain k) 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 129 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26k VAL* 3.6 3.7 - - - +
71k MET* 5.3 8.1 - - + -
73k PHE* 5.4 1.6 - - + -
74k ALA 3.4 8.5 - - - +
75k GLY* 4.2 2.0 - - - -
76k LEU 3.1 33.0 - - - +
79k ASP* 3.8 4.5 - - + -
80k ALA* 3.5 34.8 - - + +
83k VAL* 4.1 22.9 - - + -
115k LYS* 3.5 26.6 + - - +
127k PHE* 3.1 14.2 + - + +
128k GLY* 1.3 83.4 - - - +
130k SER* 1.3 66.1 + - - +
131k ALA* 5.4 0.4 - - + -
149k PRO* 3.3 19.1 - - - +
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Residues in contact with SER 130 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26k VAL* 3.3 24.0 - - - +
73k PHE* 3.3 5.2 - - - +
74k ALA 2.9 31.8 + - - -
115k LYS* 4.0 2.2 - - - +
129k ILE* 1.3 71.6 - - - +
131k ALA* 1.3 63.4 + - - +
146k GLN* 4.6 1.7 + - - -
147k THR 3.6 15.8 + - - -
148k ASP* 4.0 3.3 + - - -
149k PRO* 3.4 20.3 - - - +
161k ILE* 3.7 21.6 - - - +
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Residues in contact with ALA 131 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71k MET* 3.9 27.6 - - + -
72k ALA 3.5 10.1 - - - +
73k PHE* 4.7 1.1 - - + -
111k ILE* 5.4 2.7 - - + -
115k LYS* 4.2 5.4 - - - +
129k ILE* 5.4 1.8 - - + -
130k SER* 1.3 78.6 - - - +
132k LEU* 1.3 62.9 + - - +
133k ILE* 3.8 9.2 + - + +
146k GLN* 3.3 10.0 - - - +
147k THR* 3.2 39.2 + - - +
161k ILE* 4.4 1.8 - - - -
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Residues in contact with LEU 132 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32k ALA* 3.7 21.5 - - + +
33k VAL* 3.6 33.2 - - - +
34k GLY* 3.8 2.5 - - - +
43k LEU* 5.7 0.7 - - + -
71k MET* 3.3 4.2 - - - -
72k ALA* 2.9 45.3 + - + +
131k ALA* 1.3 72.4 - - - +
133k ILE* 1.3 62.5 + - - +
134k VAL* 3.8 7.3 + - + +
144k LEU* 3.7 27.1 - - + -
145k TYR 3.8 0.2 - - - -
146k GLN* 3.7 25.8 - - + +
159k ASN* 4.5 12.6 - - + +
160k ALA* 4.8 0.9 - - - -
161k ILE* 3.9 18.7 - - + +
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Residues in contact with ILE 133 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65k LEU* 4.6 2.7 - - + -
69k VAL* 3.6 25.1 - - + -
70k CYS 3.8 3.4 - - - +
71k MET* 4.2 17.7 - - - -
104k VAL* 3.8 13.8 - - + +
107k ILE* 4.1 4.9 - - + -
108k THR* 3.4 37.5 - - + +
111k ILE* 3.5 26.9 - - + -
131k ALA* 3.8 7.6 - - + +
132k LEU* 1.3 75.7 - - - +
134k VAL* 1.3 66.1 + - - +
143k ARG 4.1 0.3 - - - +
144k LEU* 3.4 1.0 - - - -
145k TYR* 2.9 39.2 + - + +
147k THR* 4.5 9.0 - - + -
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Residues in contact with VAL 134 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34k GLY* 5.5 2.2 - - - -
35k VAL 6.1 0.7 - - - +
41k VAL* 3.7 39.7 - - + +
42k VAL 5.7 1.1 - - - +
43k LEU* 4.5 19.7 - - + -
69k VAL* 3.4 5.5 - - - +
70k CYS* 2.9 54.8 + - - +
104k VAL* 4.2 0.7 - - - -
132k LEU* 3.8 8.0 + - + +
133k ILE* 1.3 81.5 - - - +
135k GLY* 1.3 62.1 + - - +
143k ARG 3.6 4.3 - - - +
144k LEU* 3.5 23.8 - - + -
211k MET* 5.4 0.4 - - + -
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Residues in contact with GLY 135 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41k VAL* 4.8 2.4 - - - +
68k ASN 3.7 11.7 - - - -
69k VAL* 4.3 1.6 - - - -
104k VAL* 3.6 18.3 - - - +
134k VAL* 1.3 80.3 - - - +
136k PHE* 1.3 68.8 + - - -
142k PRO* 3.5 4.3 - - - +
143k ARG 2.9 34.3 + - - +
211k MET* 6.1 1.8 - - - -
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Residues in contact with PHE 136 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38k ARG 3.9 7.0 - - - -
39k ASP* 3.5 29.6 - - - -
40k ILE* 3.9 2.0 - - - -
41k VAL* 3.4 32.3 - - + -
68k ASN* 3.6 27.3 + - - +
102k VAL 5.4 0.5 - - - +
104k VAL* 4.1 4.0 - - - +
135k GLY* 1.3 73.8 - - - -
137k ASP* 1.3 64.2 + - - +
138k PHE 4.0 0.2 + - - -
140k GLY* 3.3 31.0 - - - -
141k THR 3.9 1.1 - - - -
142k PRO* 3.5 22.2 - - + -
211k MET* 3.8 15.0 - - + -
213k ARG* 3.8 43.5 - - - +
214k ASP* 5.9 0.9 - - - -
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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