Contacts of the strand formed by residues 129 - 134 (chain B) in PDB entry 1RYF
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.4 9.4 - - + +
99B ILE* 3.8 30.3 - - + -
117B TYR* 4.4 9.2 - - + -
120B VAL* 4.0 22.7 - - + -
121B ARG* 3.4 33.2 - - - +
127B THR 3.5 2.0 + - - +
128B PRO* 1.3 79.2 - - - +
130B ILE* 1.3 76.6 + - - +
168B ILE* 4.1 19.5 - - + +
169B GLY 5.3 0.6 + - - -
170B ALA* 3.2 19.2 - - + +
171B VAL* 2.8 36.4 + - - +
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Residues in contact with ILE 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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96B VAL* 4.1 7.6 - - + -
97B PHE 2.8 5.9 + - - -
98B LEU* 3.4 20.3 - - + -
99B ILE 3.0 24.6 + - - -
129B ILE* 1.3 76.7 - - - +
131B LEU* 1.3 64.4 + - - +
132B VAL* 3.8 16.7 + - + +
171B VAL* 3.8 25.4 - - + -
172B LYS* 3.7 20.2 - - + +
174B LEU* 4.1 21.8 - - + -
187B VAL 4.8 3.4 - - - +
190B GLU 4.1 19.3 - - - +
191B ALA* 4.0 18.4 - - - -
194B ALA* 4.3 3.6 - - + -
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Residues in contact with LEU 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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99B ILE* 3.4 19.5 - - + +
101B PHE* 3.9 20.6 - - + -
112B VAL* 3.6 26.0 - - + -
129B ILE* 4.8 1.1 - - - -
130B ILE* 1.3 73.5 - - - +
132B VAL* 1.3 61.1 + - - +
161B GLY 3.6 12.1 - - - +
164B MET* 3.9 14.8 - - + +
165B ALA* 3.6 30.3 - - + +
168B ILE* 4.3 4.7 - - + -
170B ALA* 4.0 13.1 - - + +
172B LYS 3.0 13.1 + - - +
173B TYR* 3.3 14.9 - - + -
174B LEU 3.0 25.8 + - - -
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Residues in contact with VAL 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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19B LEU* 4.9 3.1 - - + -
98B LEU* 4.4 13.5 - - + -
99B ILE 2.9 10.9 + - - +
100B CYS* 3.2 12.4 - - - -
101B PHE* 3.0 31.1 + - - +
130B ILE* 4.0 23.1 - - + +
131B LEU* 1.3 77.8 - - - +
133B GLY* 1.3 64.0 + - - +
134B THR* 3.8 8.2 + - + -
174B LEU* 3.2 7.9 - - + +
176B CYS* 3.9 28.0 - - - -
187B VAL* 4.0 27.1 - - + -
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Residues in contact with GLY 133 (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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101B PHE* 3.4 26.9 - - - -
103B LEU* 3.8 14.9 - - - +
132B VAL* 1.3 72.3 - - - +
134B THR* 1.3 59.0 + - - -
173B TYR* 4.0 4.9 - - - -
174B LEU 2.8 13.0 + - - +
175B GLU* 3.2 2.8 - - - -
176B CYS* 2.8 31.7 + - - +
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Residues in contact with THR 134 (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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14B VAL 2.7 28.5 + - - +
15B GLY* 5.0 8.3 - - - +
19B LEU* 4.8 7.6 - - + -
100B CYS* 4.3 15.9 - - + -
101B PHE 2.9 19.1 + - - +
102B SER* 3.2 6.8 - - - -
103B LEU* 2.8 26.7 + - - +
132B VAL* 4.1 19.1 - - + +
133B GLY* 1.3 74.3 - - - -
135B LYS* 1.3 69.1 + - - +
136B LEU 3.3 3.4 + - - -
176B CYS* 3.5 11.7 - - - -
178B ALA 6.3 0.4 - - - -
1538B GDP 5.8 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