Contacts of the strand formed by residues 127 - 132 (chain B) in PDB entry 5GQQ
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 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B VAL* 3.5 27.4 - - + -
50B SER 3.4 6.3 - - - +
51B THR* 3.6 20.2 - - + +
68B LYS* 4.0 21.3 - - + +
69B LEU* 4.3 4.0 - - + -
72B TYR* 4.6 8.3 - - + -
122B PRO* 3.2 31.5 - - + +
124B GLU* 3.2 33.8 + - + +
125B SER 3.3 3.1 - - - +
126B ASP* 1.3 78.9 - - - +
128B PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B VAL* 3.6 2.4 - - - +
50B SER* 2.8 66.4 + - - -
52B SER* 3.9 24.5 - - - -
106B THR* 4.3 5.2 - - + -
122B PRO* 4.2 4.0 - - - -
125B SER 5.8 1.3 - - - +
126B ASP 3.7 14.6 - - - -
127B VAL* 1.3 75.1 - - - +
129B ILE* 1.3 77.7 + - - +
130B GLU* 4.1 14.4 - - + -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS* 4.0 30.1 - - + -
48B TRP 3.5 5.4 - - - +
49B VAL* 4.2 10.5 - - + -
72B TYR* 3.8 22.2 - - + +
111B ILE* 4.0 15.7 - - + -
119B PRO* 4.3 13.5 - - + +
120B PRO 4.0 6.5 - - - +
121B ARG* 5.2 2.2 - - + -
122B PRO* 4.0 21.0 - - + +
128B PHE* 1.3 80.7 - - - +
130B GLU* 1.3 66.3 + - - +
131B ASP* 4.0 5.0 + - - +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS* 3.3 7.4 - - - +
48B TRP* 2.7 40.0 + - + +
50B SER* 2.9 24.4 + - - +
106B THR* 5.0 3.8 - - - +
108B SER* 3.7 1.4 + - - -
128B PHE* 3.6 16.1 + - + -
129B ILE* 1.3 74.1 - - - +
131B ASP* 1.3 66.6 + - - +
132B ARG* 3.0 54.6 + - - +
175B TYR* 4.5 4.5 + - - -
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA 4.0 3.1 - - - -
47B LYS* 3.2 42.4 + - - +
129B ILE* 4.0 5.4 + - - +
130B GLU* 1.3 74.3 - - - +
132B ARG* 1.3 64.5 + - - +
133B ALA* 3.2 5.0 + - - +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B TYR* 6.3 0.9 - - - -
44B GLY 5.8 1.3 - - - +
45B PRO* 3.2 4.0 - - - +
46B ALA 2.9 42.5 + - - +
48B TRP* 3.3 45.7 - - + +
90B THR* 3.4 18.4 + - - +
92B TYR* 5.9 1.0 - - - +
108B SER* 3.2 34.6 + - - -
130B GLU* 3.0 32.6 + - - +
131B ASP* 1.3 71.7 - - - +
133B ALA* 1.3 74.4 + - - +
135B MET* 4.0 20.2 - - + +
175B TYR* 3.8 28.2 + - - +
193B TRP* 4.6 5.5 - - - -
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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
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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