Contacts of the strand formed by residues 139 - 147 (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 VAL 139 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F ILE* 4.0 6.5 - - - +
78F MET* 4.3 2.2 - - + -
79F SER 3.3 17.3 - - - +
81F LEU 4.2 9.4 - - - +
84F ASP* 4.6 0.7 - - + -
85F ALA* 3.8 29.6 - - + +
88F LEU* 3.6 29.8 - - + -
137F PHE* 3.1 16.2 + - + +
138F GLY* 1.3 79.3 - - - +
140F ALA* 1.3 72.1 + - - +
141F LEU* 4.0 11.2 - - + +
156F MET* 4.4 4.0 - - + +
157F ASP* 4.3 1.4 - - - -
158F PRO* 3.2 22.0 - - - +
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Residues in contact with ALA 140 (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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31F ILE* 3.6 32.4 - - + +
78F MET* 3.4 3.1 - - - -
79F SER* 2.9 33.4 + - - +
139F VAL* 1.3 75.1 - - - +
141F LEU* 1.3 62.9 + - - +
155F HIS* 4.5 4.5 - - + -
156F MET 3.3 11.4 - - - +
157F ASP* 4.9 0.2 - - - -
170F ILE* 3.7 24.7 - - + +
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Residues in contact with LEU 141 (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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76F CYS* 3.6 15.9 - - - -
77F ALA 3.5 2.5 - - - -
78F MET* 3.6 29.4 - - + -
85F ALA* 4.8 1.8 - - + -
88F LEU* 3.9 23.3 - - + -
89F ILE* 4.2 9.4 - - + -
116F VAL* 4.3 3.4 - - + -
139F VAL* 4.0 10.3 - - + -
140F ALA* 1.3 76.0 - - - +
142F LEU* 1.3 65.4 + - - +
143F PHE* 3.7 32.3 - - + -
155F HIS* 3.4 5.9 + - - -
156F MET* 2.9 60.0 + - + +
170F ILE* 4.3 0.7 - - - -
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Residues in contact with LEU 142 (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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37F ALA* 4.1 7.9 - - + +
38F ILE 4.1 6.3 - - - +
39F GLY* 3.9 26.0 - - - +
48F LEU* 4.0 17.4 - - + +
76F CYS* 3.3 3.9 - - - -
77F ALA* 2.8 36.2 + - + +
141F LEU* 1.3 80.5 - - - +
143F PHE* 1.3 62.8 + - - +
144F GLY 3.8 0.7 + - - -
153F LEU* 4.3 7.6 - - + -
154F PHE 3.3 12.3 - - - +
155F HIS* 3.8 21.8 - - + +
168F ARG* 4.0 22.4 - - + +
170F ILE* 3.7 26.5 - - + -
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Residues in contact with PHE 143 (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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70F ILE* 4.0 20.6 - - + -
74F ILE* 4.5 5.6 - - + -
75F GLY 3.4 5.2 - - - -
76F CYS* 3.6 28.9 - - + -
89F ILE* 4.7 3.4 - - + -
92F ALA* 4.7 2.2 - - + -
109F VAL* 4.5 10.0 - - + +
112F VAL* 4.8 5.8 - - + -
113F THR* 3.8 33.9 - - + +
116F VAL* 3.8 33.2 - - + -
141F LEU* 3.7 34.1 - - + -
142F LEU* 1.3 75.5 - - - +
144F GLY* 1.3 60.5 + - - +
152F GLN 4.0 0.5 - - - +
153F LEU* 3.3 6.6 - - - +
154F PHE* 2.9 37.3 + - + +
156F MET* 4.7 8.5 - - + -
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Residues in contact with GLY 144 (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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46F VAL* 4.1 22.4 - - - -
48F LEU* 4.5 7.6 - - - +
74F ILE* 3.5 3.2 - - - +
75F GLY* 2.8 40.3 + - - -
109F VAL* 4.8 0.2 - - - -
142F LEU 3.8 1.6 + - - -
143F PHE* 1.3 74.6 - - - +
145F GLY* 1.3 57.6 + - - -
152F GLN 3.7 5.4 - - - -
153F LEU* 4.3 2.0 - - - -
220F VAL* 4.0 9.2 - - - +
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Residues in contact with GLY 145 (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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46F VAL* 3.9 3.8 - - - +
73F HIS 3.2 12.3 - - - -
74F ILE* 4.2 2.5 - - - -
109F VAL* 3.6 21.9 - - - +
143F PHE 4.2 0.6 - - - -
144F GLY* 1.3 74.2 - - - +
146F VAL* 1.3 67.1 + - - +
151F PRO* 3.4 4.2 - - - +
152F GLN 2.9 32.1 + - - +
220F VAL* 5.0 1.3 - - - -
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Residues in contact with VAL 146 (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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46F VAL* 5.3 0.7 - - + -
73F HIS* 3.2 36.1 + - + +
109F VAL* 3.8 2.4 - - - +
145F GLY* 1.3 80.5 - - - +
147F ASP* 1.3 71.0 + - - +
150F GLY* 3.5 8.1 - - - +
151F PRO* 4.5 9.9 - - + -
220F VAL* 3.6 39.5 - - + +
221F GLN 4.1 7.0 - - - +
222F PRO* 4.0 30.3 - - + +
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Residues in contact with ASP 147 (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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73F HIS* 5.1 0.7 - - + -
106F THR* 5.1 5.8 - - - +
107F MET 4.7 4.5 - - - +
108F THR* 3.5 20.5 - - - -
109F VAL* 3.0 28.0 + - + +
146F VAL* 1.3 83.7 - - - +
148F GLU* 1.3 67.0 + - - +
149F LYS* 3.1 24.4 + - - +
150F GLY* 2.9 28.4 + - - +
152F GLN* 3.1 17.0 - - - +
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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