Contacts of the strand formed by residues 94 - 99 (chain A) in PDB entry 1R1P
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 PHE 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A TRP* 4.1 22.0 - + - -
61A PHE* 4.1 12.1 - + - -
84A ILE* 4.0 15.9 - - + -
85A ARG 3.4 16.6 - - - -
86A ALA* 3.9 13.5 - - + -
92A GLY 4.8 0.9 - - - -
93A ASP* 1.3 81.2 - - - +
95A SER* 1.3 63.2 + - - +
108A LYS* 3.9 1.7 - - - -
109A VAL* 3.0 46.2 + - + +
127A LEU* 5.5 2.0 - - + -
86B ALA* 4.2 17.5 - - + -
92B GLY* 3.5 42.2 - - - +
93B ASP 4.1 2.0 - - - -
94B PHE* 3.3 32.8 - + - -
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Residues in contact with SER 95 (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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83A ILE 3.8 0.5 - - - +
84A ILE* 3.4 5.2 - - - +
85A ARG* 2.8 63.4 + - - +
87A SER* 3.8 6.5 - - - -
94A PHE* 1.3 76.5 + - - +
96A ILE* 1.3 64.5 + - - +
97A SER 4.1 0.2 - - - -
107A PHE 3.3 9.4 - - - -
108A LYS* 4.9 2.8 + - - -
109A VAL* 4.7 0.4 - - - +
558E PTR 2.7 34.5 + - - -
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Residues in contact with ILE 96 (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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82A PHE* 4.1 19.1 - - + -
83A ILE 3.5 8.1 - - - +
84A ILE* 3.9 21.3 - - + -
95A SER* 1.3 77.3 - - - +
97A SER* 1.3 62.9 + - - +
98A VAL* 3.8 19.5 - - + -
106A HIS* 3.4 2.1 - - - -
107A PHE* 2.8 50.5 + - + +
109A VAL* 3.8 25.6 - - + -
119A LEU* 4.5 11.2 - - + -
127A LEU* 4.8 1.8 - - + -
130A LEU* 4.1 23.3 - - + -
131A VAL* 5.0 3.6 - - + -
139A ILE* 4.8 6.5 - - + -
147A LEU* 4.8 4.5 - - + -
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Residues in contact with SER 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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70A ALA* 3.7 10.5 - - - +
74A LEU* 3.4 18.0 - - - +
82A PHE* 3.1 8.0 - - - +
83A ILE 2.9 33.4 + - - -
85A ARG* 2.9 24.9 + - - -
95A SER 4.1 0.2 - - - -
96A ILE* 1.3 70.2 - - - +
98A VAL* 1.3 61.6 + - - +
104A VAL* 4.3 1.8 - - - -
105A GLN 3.4 5.4 - - - -
106A HIS* 2.8 30.8 + - - -
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Residues in contact with VAL 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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80A GLY* 4.3 3.6 - - - -
81A PHE 3.5 8.7 - - - +
82A PHE* 4.1 0.2 - - + -
96A ILE* 3.8 15.0 - - + -
97A SER* 1.3 78.6 - - - +
99A ARG* 1.3 71.9 + - - +
100A HIS* 2.9 31.8 + - + -
104A VAL* 4.0 5.5 - - - +
105A GLN 2.8 25.0 + - - +
107A PHE* 3.8 18.2 - - + -
139A ILE* 4.2 4.0 - - + -
145A VAL* 3.9 21.1 - - + -
147A LEU* 3.8 30.1 - - + -
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Residues in contact with ARG 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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74A LEU* 3.0 26.9 + - + +
75A MET* 2.9 37.0 + - - +
77A LYS 3.0 19.2 + - - +
78A ASP* 3.4 30.3 - - - +
79A ILE* 3.5 3.1 - - - +
80A GLY 2.8 25.3 + - - -
81A PHE* 2.9 16.1 + - + +
98A VAL* 1.3 75.0 - - - +
100A HIS* 1.3 81.2 + - - +
101A GLU 3.2 18.8 + - - -
102A ASP* 3.8 13.5 - - - +
103A ASP 3.6 7.8 - - - +
104A VAL* 3.8 11.9 - - - -
145A VAL* 4.0 1.4 - - - +
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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