Contacts of the helix formed by residues 97 - 106 (chain A) in PDB entry 1RA3
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 GLY 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.8 13.7 - - - +
96A GLY* 1.4 70.5 - - - +
98A ARG* 1.4 61.1 + - - -
100A TYR* 3.3 4.1 + - - +
101A GLU* 3.0 25.4 + - - +
123A THR* 3.6 24.7 - - - +
124A HIS 4.3 8.2 - - - +
126A PRO* 5.1 0.5 - - - +
164A NAP 2.8 12.5 + - - -
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Residues in contact with ARG 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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97A GLY* 1.4 72.5 - - - +
99A VAL* 1.4 64.5 + - - +
101A GLU* 3.4 10.6 + - - +
102A GLN* 3.1 38.1 + - - +
164A NAP 3.0 104.9 + - + +
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Residues in contact with VAL 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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41A ILE* 4.4 6.1 - - + +
43A GLY* 3.4 26.0 - - - +
62A LEU* 4.1 9.4 - - + -
93A VAL* 3.6 25.6 - - + -
95A GLY 3.4 14.1 - - - +
96A GLY 3.0 3.7 + - - +
98A ARG* 1.4 74.7 - - - +
100A TYR* 1.3 66.8 + - - +
102A GLN* 2.9 16.3 + - - +
103A PHE* 3.0 35.8 + - + -
164A NAP 3.4 30.9 + - + +
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Residues in contact with TYR 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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4A LEU* 4.1 15.2 - - + +
5A ILE 2.6 25.7 + - - -
6A ALA* 3.3 20.8 - - + +
14A ILE* 3.5 33.2 - - + -
93A VAL* 3.6 17.0 - - + -
94A ILE 3.0 13.2 + - - -
95A GLY* 3.4 28.4 - - - -
96A GLY* 2.8 22.7 + - - +
97A GLY 3.7 2.9 - - - +
99A VAL* 1.3 73.0 - - - +
101A GLU* 1.3 63.5 + - - +
103A PHE* 4.6 2.0 - - - +
104A LEU* 2.8 29.5 + - - +
125A PHE* 3.8 17.7 - + + -
126A PRO* 3.7 19.7 - - + -
161A MTX 3.3 4.2 + - - -
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Residues in contact with GLU 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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97A GLY 3.0 17.4 + - - +
98A ARG* 3.7 10.7 - - - +
100A TYR* 1.3 79.1 - - - +
102A GLN* 1.3 67.1 + - + +
104A LEU* 4.4 0.5 - - - +
105A PRO* 3.4 17.2 - - - +
126A PRO* 4.1 16.1 - - + +
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Residues in contact with GLN 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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62A LEU* 5.4 1.2 - - - +
78A VAL* 3.3 27.7 - - + +
98A ARG* 3.1 31.5 + - - +
99A VAL* 2.9 9.3 + - - +
101A GLU* 1.3 83.3 - - + +
103A PHE* 1.3 63.7 + - + +
105A PRO* 3.7 10.8 - - - +
106A LYS* 4.5 9.2 - - - +
164A NAP 2.9 50.2 + - - -
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Residues in contact with PHE 103 (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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2A ILE* 4.4 12.9 - - + +
4A LEU* 4.0 17.9 - - + -
41A ILE* 4.1 27.4 - - + -
62A LEU* 4.0 13.5 - - + -
78A VAL* 4.0 27.1 - - + -
81A ALA* 4.2 9.9 - - + -
82A ILE* 4.0 23.6 - - + -
93A VAL* 4.0 16.2 - - + -
99A VAL* 3.0 47.0 + - + +
100A TYR 4.2 0.7 - - - +
102A GLN* 1.3 80.7 - - + +
104A LEU* 1.4 55.9 + - - +
105A PRO* 3.2 4.0 - - - -
106A LYS* 2.6 41.2 + - + +
107A ALA* 3.2 8.3 + - - +
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Residues in contact with LEU 104 (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 LEU* 3.8 25.1 - - + +
100A TYR 2.8 20.5 + - - +
101A GLU 4.4 1.3 - - - +
103A PHE* 1.4 68.1 - - - +
105A PRO* 1.3 73.4 - - + +
106A LYS 2.8 1.9 + - - -
107A ALA* 2.9 10.5 + - + +
110A LEU* 4.0 19.5 - - + -
125A PHE* 4.7 5.6 - - + -
126A PRO* 3.7 29.6 - - + +
127A ASP 4.0 14.6 - - - +
128A TYR* 4.6 9.2 - - + -
133A TRP* 4.2 14.6 - - + -
158A ARG* 2.8 21.7 + - - +
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Residues in contact with PRO 105 (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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101A GLU 3.4 15.9 - - - +
102A GLN 3.7 9.9 - - - +
103A PHE 3.2 4.9 - - - -
104A LEU* 1.3 98.2 - - + +
106A LYS* 1.3 60.3 + - + +
158A ARG* 4.1 12.2 + - - +
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Residues in contact with LYS 106 (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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2A ILE* 3.9 26.2 + - + +
78A VAL* 4.7 8.2 - - + +
79A ASP* 4.9 7.7 + - - -
82A ILE* 3.3 34.6 - - + +
102A GLN 4.5 9.6 - - - +
103A PHE* 2.6 29.0 + - + +
105A PRO* 1.3 79.9 - - + +
107A ALA* 1.3 61.7 + - - +
108A GLN* 3.9 10.5 + - - +
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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