Contacts of the strand formed by residues 96 - 102 (chain A) 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 VAL 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ILE* 4.3 6.5 - - + -
5A LYS 3.7 2.9 - - - +
6A CYS* 3.3 27.2 - - + -
7A VAL 3.1 22.2 + - - -
94A ALA* 3.4 4.5 - - - +
95A ASP* 1.3 79.2 - - - +
97A PHE* 1.3 74.6 + - - +
98A LEU* 5.1 0.2 - - + -
127A THR* 3.9 1.6 - - - -
128A PRO* 3.5 23.8 - - + +
130A ILE* 4.1 17.5 - - + -
191A ALA* 3.9 28.0 - - + +
194A ALA* 4.4 1.6 - - + -
195A VAL* 3.9 12.1 - - + -
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.3 39.5 - - + -
9A VAL* 4.8 6.5 - - + -
94A ALA* 3.7 15.5 - - + -
96A VAL* 1.3 77.5 - - - +
98A LEU* 1.3 65.9 + - - +
99A ILE* 4.9 1.6 - - + -
120A VAL* 3.6 45.5 - - + -
123A HIS* 5.9 1.8 - - + -
124A CYS* 3.8 26.5 - - - -
127A THR* 3.5 25.4 - - + -
128A PRO 3.0 11.2 + - - +
129A ILE* 3.4 11.7 - - + -
130A ILE* 2.8 26.7 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A CYS* 3.6 19.7 - - - -
7A VAL 3.0 7.4 + - - +
8A VAL* 3.5 23.2 - - + +
9A VAL* 3.0 27.2 + - - +
19A LEU* 4.0 13.5 - - + -
97A PHE* 1.3 74.3 - - - +
99A ILE* 1.3 61.6 + - - +
100A CYS* 4.3 5.2 - - - -
130A ILE* 3.5 31.6 - - + -
132A VAL* 4.3 4.7 - - + -
187A VAL* 3.9 20.9 - - + -
188A PHE* 3.8 28.0 - - + -
191A ALA* 4.1 11.2 - - + -
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.5 18.2 - - + +
97A PHE* 4.0 2.4 - - + -
98A LEU* 1.3 73.0 - - - +
100A CYS* 1.3 63.7 + - - +
112A VAL* 4.1 26.7 - - + +
116A TRP* 3.8 27.1 - - + +
117A TYR* 3.8 30.7 - - - +
120A VAL* 4.2 7.6 - - + -
129A ILE* 3.8 31.9 - - + -
130A ILE 3.0 9.8 + - - +
131A LEU* 3.5 9.5 - - + +
132A VAL 2.9 24.1 + - - -
168A ILE* 4.4 6.3 - - + -
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Residues in contact with CYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.8 28.9 - - - -
9A VAL 2.8 11.2 + - - +
10A GLY* 3.4 18.7 - - - -
11A ASP 4.1 1.9 + - - -
14A VAL* 3.9 19.6 - - + +
16A LYS* 4.3 6.3 - - + -
19A LEU* 4.2 15.7 - - - -
98A LEU* 4.3 5.4 - - - -
99A ILE* 1.3 79.7 - - - +
101A PHE* 1.3 62.6 + - - +
108A SER 5.0 1.2 - - - +
112A VAL* 4.8 1.6 - - - +
116A TRP* 5.0 1.0 - - - -
132A VAL* 3.2 23.6 - - - +
134A THR* 4.3 9.2 - - + -
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Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.1 6.5 - - - -
100A CYS* 1.3 73.1 - - - +
102A SER* 1.3 72.9 + - - +
103A LEU* 3.7 19.3 - - + -
108A SER* 3.4 29.2 - - - +
109A PHE* 3.4 38.6 - + + -
112A VAL* 3.7 17.9 - - + -
131A LEU* 3.8 15.7 - - + -
132A VAL 3.0 12.4 + - - +
133A GLY* 3.7 21.1 - - - -
134A THR* 2.8 28.0 + - - -
156A ILE* 4.0 8.5 - - + -
173A TYR* 3.7 26.5 - + - -
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 5.1 0.2 - - - -
14A VAL* 3.7 20.6 - - - +
101A PHE* 1.3 80.3 - - - +
103A LEU* 1.4 57.3 + - - +
104A VAL* 3.2 26.5 + - - +
105A SER* 2.9 38.1 + - - +
108A SER* 2.9 11.5 + - - -
134A THR* 3.2 13.9 + - - -
135A LYS* 3.7 14.6 + - - +
156A ILE* 4.6 0.5 - - - +
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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