Contacts of the strand formed by residues 140 - 144 (chain l) 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 ALA 140 (chain l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31l ILE* 3.7 30.4 - - + +
78l MET* 3.5 3.5 - - - -
79l SER 2.9 32.4 + - - +
139l VAL* 1.3 75.3 - - - +
141l LEU* 1.3 61.2 + - - +
155l HIS* 4.8 2.9 - - + -
156l MET 4.4 11.7 - - - -
157l ASP* 4.8 1.6 - - + -
170l ILE* 3.6 28.5 - - + +
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Residues in contact with LEU 141 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76l CYS* 3.6 18.6 - - - -
77l ALA 3.5 1.1 - - - -
78l MET* 3.5 32.5 - - + -
85l ALA* 4.8 2.7 - - + -
88l LEU* 4.0 22.4 - - + -
89l ILE* 4.5 3.8 - - + -
116l VAL* 4.1 3.6 - - + -
139l VAL* 4.0 10.1 - - + -
140l ALA* 1.3 78.1 - - - +
142l LEU* 1.3 67.1 + - - +
143l PHE* 3.9 32.1 - - + -
154l PHE 3.9 0.2 - - - +
155l HIS* 3.5 5.4 + - - -
156l MET* 2.9 57.1 + - - +
170l ILE* 4.4 0.2 - - - -
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Residues in contact with LEU 142 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37l ALA* 4.1 12.8 - - + +
38l ILE 4.2 3.6 - - - -
39l GLY* 3.9 25.8 - - - +
48l LEU* 4.1 14.8 - - + +
75l GLY 3.8 0.3 - - - +
76l CYS* 3.3 3.9 - - - -
77l ALA* 2.9 41.0 + - + +
141l LEU* 1.3 82.5 - - - +
143l PHE* 1.3 63.4 + - - +
144l GLY 3.9 0.3 + - - -
153l LEU* 4.4 7.9 - - + -
154l PHE 3.3 6.5 - - - +
155l HIS* 3.7 28.9 - - + +
168l ARG* 4.1 18.4 - - + +
170l ILE* 3.7 26.5 - - + -
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Residues in contact with PHE 143 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70l ILE* 4.0 23.8 - - + -
74l ILE* 4.4 3.6 - - + -
75l GLY 3.4 2.7 - - - +
76l CYS* 3.6 24.2 - - + -
89l ILE* 5.1 2.5 - - + -
92l ALA* 4.7 1.1 - - + -
109l VAL* 4.2 11.1 - - + +
112l VAL* 4.2 16.4 - - + -
113l THR* 3.7 38.4 - - + +
116l VAL* 3.8 28.3 - - + -
141l LEU* 3.9 34.5 - - + -
142l LEU* 1.3 75.9 - - - +
144l GLY* 1.3 59.1 + - - +
152l GLN 4.1 0.5 - - - +
153l LEU* 3.3 5.3 - - - +
154l PHE 2.8 39.1 + - - +
156l MET* 4.9 4.7 - - - -
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Residues in contact with GLY 144 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46l VAL* 4.3 10.3 - - - -
48l LEU* 4.7 7.0 - - - +
74l ILE* 3.4 3.8 - - - +
75l GLY* 2.8 37.2 + - - -
109l VAL* 4.7 0.2 - - - -
142l LEU 3.9 1.0 + - - -
143l PHE* 1.3 74.7 - - - +
145l GLY* 1.3 57.5 + - - -
152l GLN 3.6 6.5 - - - -
153l LEU* 4.1 9.6 - - - -
220l VAL* 3.8 11.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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