Contacts of the strand formed by residues 125 - 130 (chain A) in PDB entry 1RFA
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 GLU 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ARG* 2.6 54.8 + - + +
61A PHE* 4.0 12.8 - - + -
100A ARG* 3.6 6.6 - - - +
101A LEU* 2.9 46.7 + - + +
103A HIS* 2.6 37.0 + - - +
124A GLU* 1.3 74.8 - - - +
126A LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 126 (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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58A ILE* 3.0 50.9 - - + -
59A ARG 2.8 16.4 + - - +
60A VAL* 4.2 7.9 - - + -
61A PHE* 2.8 31.3 + - - +
78A LEU* 4.0 10.5 - - + -
82A LEU* 5.4 3.8 - - + -
98A VAL* 3.5 16.4 - - + -
99A PHE 3.1 11.0 - - - +
100A ARG* 4.1 5.6 - - + +
101A LEU* 3.9 3.6 - - - +
112A LEU* 3.3 31.2 - - + -
118A ALA* 6.0 0.4 - - + -
121A LEU* 4.0 12.6 - - + -
124A GLU* 5.0 0.2 - - + -
125A GLU* 1.3 76.3 - - - +
127A GLN* 1.3 62.3 + - - +
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Residues in contact with GLN 127 (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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60A VAL* 5.0 1.1 - - - -
61A PHE* 3.3 30.5 - - + +
62A LEU 4.2 8.1 + - - +
63A PRO* 4.5 2.6 - - - +
65A LYS* 6.6 0.2 - - - -
98A VAL* 3.4 7.0 - - - +
99A PHE* 2.7 30.3 + - - +
101A LEU* 3.4 18.3 - - + +
109A LYS* 2.7 32.7 + - + +
126A LEU* 1.3 71.8 - - - +
128A VAL* 1.3 85.3 + - - +
129A ASP* 2.8 22.6 + - - -
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Residues in contact with VAL 128 (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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60A VAL* 4.3 8.7 - - + -
61A PHE 2.9 8.7 + - - +
62A LEU* 5.1 0.2 - - - -
63A PRO* 3.1 34.5 - - + +
82A LEU* 3.8 29.2 - - + -
86A LEU* 4.5 16.2 - - + -
96A CYS* 3.2 33.4 - - + -
97A ALA 3.4 4.9 - - - +
98A VAL* 3.9 8.7 - - + -
114A TRP* 4.8 4.3 - - + -
127A GLN* 1.3 98.2 + - - +
129A ASP* 1.3 61.6 + - - +
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Residues in contact with ASP 129 (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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63A PRO* 4.0 15.4 - - - +
96A CYS* 3.1 15.0 - - - +
97A ALA 2.6 21.3 + - - -
99A PHE* 3.7 23.1 - - + -
109A LYS* 2.7 28.1 + - - -
127A GLN* 2.8 11.2 + - - +
128A VAL* 1.3 73.0 - - - +
130A PHE* 1.3 95.4 + - + +
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Residues in contact with PHE 130 (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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63A PRO* 5.2 0.6 - - - +
95A CYS 4.5 2.5 - - - +
96A CYS* 4.0 2.9 - - - +
97A ALA* 3.0 15.3 + - - +
99A PHE* 4.7 5.2 - + - -
129A ASP* 1.3 102.5 + - + +
131A LEU* 1.3 87.9 + - + +
132A ASP* 5.5 2.0 - - - -
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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