Contacts of the strand formed by residues 116 - 121 (chain B) in PDB entry 1RGQ
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 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ALA* 3.5 32.2 - - + +
152A HIS* 2.8 35.4 + - + +
6B ILE* 3.8 30.7 - - + +
7B THR* 4.8 5.8 - - - -
8B ALA* 4.8 5.8 - - + +
108B TYR* 3.7 30.7 - - + -
109B LEU 3.3 7.0 - - - +
110B VAL* 4.7 8.1 - - + -
114B ALA 4.8 4.7 - - - +
115B ASP* 1.3 77.1 - - - +
117B ILE* 1.3 60.8 + - - +
118B PRO* 3.7 0.9 - - - +
133B ARG* 5.2 0.4 + - - -
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Residues in contact with ILE 117 (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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108B TYR* 3.4 4.0 - - - -
109B LEU* 2.8 52.4 + - + +
111B THR* 3.8 19.1 - - + -
115B ASP* 5.3 0.4 - - + -
116B VAL* 1.3 72.2 - - - +
118B PRO* 1.4 74.8 - - + +
119B VAL* 3.5 2.6 + - - +
129B LEU* 3.7 29.2 - - + -
130B LEU 5.7 0.4 - - - +
131B SER* 5.1 2.5 - - - +
133B ARG* 3.8 28.5 - - - +
137B TYR* 3.5 38.1 - - + +
138B LEU* 4.1 10.3 - - + -
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Residues in contact with PRO 118 (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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101A THR* 4.0 17.3 - - - +
102A CYS* 4.0 10.3 - - + -
150A ALA* 4.4 7.9 - - + -
152A HIS* 3.9 15.3 - - + -
193A ZN 4.1 18.4 - - - -
107B LEU 3.9 4.7 - - - +
108B TYR* 3.9 6.5 - - + -
116B VAL 3.7 5.4 - - - +
117B ILE* 1.4 91.0 - - + +
119B VAL* 1.3 62.3 + - - +
129B LEU* 3.9 0.7 - - - -
130B LEU* 3.4 46.7 + - + -
131B SER* 5.8 1.8 - - - +
133B ARG* 4.6 4.7 - - - +
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Residues in contact with VAL 119 (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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106B ASP* 3.6 3.1 - - - -
107B LEU* 2.7 55.9 + - + +
109B LEU* 4.1 18.2 - - + +
117B ILE 3.7 11.2 - - - +
118B PRO* 1.3 79.6 - - - +
120B ARG* 1.3 60.6 + - - +
121B ARG 4.9 0.2 - - - +
127B GLY* 3.9 7.2 - - - -
128B SER 3.5 24.0 - - - +
129B LEU* 3.7 19.7 - - + -
130B LEU* 4.5 4.3 - - - +
146B LEU* 4.5 9.9 - - + -
170B VAL* 3.9 21.3 - - + -
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Residues in contact with ARG 120 (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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105B SER* 2.9 36.1 + - - -
106B ASP* 2.9 36.0 + - - +
119B VAL* 1.3 73.4 - - - +
121B ARG* 1.3 78.6 + - - +
122B ARG* 3.5 28.9 + - - +
127B GLY* 3.2 3.1 - - - -
128B SER* 2.7 43.0 + - - +
130B LEU* 3.8 21.9 - - + +
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Residues in contact with ARG 121 (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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103B GLY* 5.5 4.8 + - - -
104B SER 4.4 14.2 + - - -
105B SER* 2.9 32.2 + - - +
107B LEU* 4.3 14.2 - - + +
119B VAL 4.1 0.8 + - - -
120B ARG* 1.3 81.0 - - - +
122B ARG* 1.3 64.6 + - - +
123B GLY 3.1 26.5 + - - +
124B ASP* 2.9 28.0 + - - +
126B ARG 3.7 8.5 - - - +
127B GLY* 4.1 2.0 - - - -
154B VAL* 3.7 23.2 - - - +
172B PHE* 3.8 18.6 - - + -
174B PRO* 4.2 2.2 - - - +
176B GLU* 4.1 17.4 + - - -
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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