Contacts of the strand formed by residues 71 - 77 (chain A) in PDB entry 1RLI
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS 3.6 2.0 + - - -
3A ILE* 3.3 28.9 - - + -
4A ALA 2.9 26.5 + - - +
27A PHE* 5.8 4.0 - - + -
69A CYS* 4.0 0.5 - - - +
70A HIS* 1.3 106.7 - - + +
72A LEU* 1.3 68.2 + - - +
73A ILE* 4.4 7.9 - - + -
114A GLN* 3.4 21.5 - - + +
116A TYR* 3.8 28.0 - - + +
175A LEU* 4.2 20.4 - - + -
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Residues in contact with LEU 72 (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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4A ALA* 3.6 10.1 - - + -
6A ILE* 4.4 9.2 - - + -
66A ILE* 3.8 33.7 - - + +
69A CYS* 4.1 10.5 - - + +
71A ILE* 1.3 81.3 - - - +
73A ILE* 1.3 63.9 + - - +
74A PHE* 3.9 25.2 - - + -
110A MET* 4.0 23.3 - - + -
113A LYS* 3.6 31.4 - - + -
114A GLN 2.9 8.9 + - - +
115A ALA* 3.4 6.5 - - + +
116A TYR* 3.0 25.8 + - - +
145A MET* 5.3 4.0 - - - -
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Residues in contact with ILE 73 (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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3A ILE* 5.2 1.6 - - + -
4A ALA 2.9 15.9 + - - +
5A VAL* 3.4 14.3 - - + +
6A ILE* 2.7 32.8 + - - +
20A ALA* 5.4 0.9 - - + +
23A ALA* 4.6 8.5 - - + -
24A VAL* 3.6 32.5 - - + -
71A ILE* 4.4 6.1 - - + -
72A LEU* 1.3 75.7 - - - +
74A PHE* 1.3 63.9 + - - +
75A ALA* 3.5 2.3 + - + +
116A TYR* 3.5 23.8 - - + +
118A ILE* 3.9 30.3 - - + -
174A LEU* 5.0 2.0 - - + -
175A LEU* 3.9 22.0 - - + -
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Residues in contact with PHE 74 (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 ILE* 3.7 32.3 - - + -
72A LEU* 3.9 29.6 - - + -
73A ILE* 1.3 73.1 - - - +
75A ALA* 1.3 59.6 + - - +
76A THR* 4.1 1.1 + - - +
87A LEU* 4.1 24.9 - - + -
90A PHE* 4.7 1.3 - + - -
91A ILE* 4.6 11.4 - - + -
94A TRP* 3.7 36.3 - + - -
110A MET* 5.1 0.2 - - + -
115A ALA* 4.5 3.1 - - + -
116A TYR 2.8 16.2 + - - +
117A VAL* 3.3 14.3 - - + +
118A ILE 2.9 25.8 + - - +
136A PHE* 4.4 10.1 - + + -
140A PHE* 3.6 31.9 - + - -
145A MET* 5.7 0.7 - - - -
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Residues in contact with ALA 75 (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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5A VAL* 4.1 20.6 - - + -
6A ILE 2.9 12.7 + - - +
7A ASN* 3.4 7.6 - - - +
8A GLY 2.8 27.2 + - - -
16A THR* 3.9 17.0 - - + -
20A ALA* 4.2 13.2 - - + -
73A ILE* 3.5 2.2 + - + +
74A PHE* 1.3 72.6 - - - +
76A THR* 1.3 62.6 + - - +
87A LEU* 4.9 1.4 - - - +
118A ILE* 3.2 13.2 - - + +
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Residues in contact with THR 76 (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 GLY* 4.8 0.9 - - - -
16A THR* 3.7 5.3 + - - +
74A PHE 5.2 1.6 - - - +
75A ALA* 1.3 76.3 - - - +
77A PRO* 1.3 91.2 + - - +
83A MET* 4.1 16.4 - - + -
84A SER* 2.9 23.2 + - - -
87A LEU* 3.8 18.6 - - + -
118A ILE 2.9 9.0 + - - +
119A ALA* 3.1 35.0 - - + -
120A VAL 3.2 2.1 + - - -
132A LEU* 4.8 2.2 - - + -
136A PHE* 4.6 11.4 - - + -
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Residues in contact with PRO 77 (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 GLY 4.1 1.1 - - - -
9A GLY* 4.0 25.8 - - - +
16A THR* 3.4 17.0 - - + +
76A THR* 1.3 109.4 + - - +
78A ILE* 1.3 61.2 + - - +
79A TYR* 3.6 40.2 + - + +
82A GLY 3.9 0.3 - - - +
84A SER* 3.7 9.9 + - - -
120A VAL 3.3 11.2 - - - +
606A PT 4.2 10.1 - - - -
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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