Contacts of the strand formed by residues 104 - 111 (chain B) in PDB entry 2RHM
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 THR 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B THR* 3.7 19.2 + - - +
4B PRO 2.9 11.1 + - - -
5B ALA* 3.3 11.4 - - + +
6B LEU 3.0 20.1 + - - -
103B PHE* 1.3 73.9 - - - +
105B PRO* 1.4 72.4 - - + +
106B ILE* 3.8 6.2 + - + +
160B PRO* 6.1 1.3 - - + -
184B HIS 6.2 0.2 - - - +
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Residues in contact with PRO 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU 3.4 6.5 - - - +
8B ILE* 4.1 9.6 - - + -
98B HIS* 5.8 0.7 - - + -
103B PHE* 3.8 25.1 - - + +
104B THR* 1.4 91.1 - - + +
106B ILE* 1.3 66.1 + - - +
107B GLN* 5.8 0.9 - - + -
157B LEU* 3.7 30.7 - - + +
158B GLY 3.5 22.2 - - - +
159B GLY* 3.8 2.8 - - - -
160B PRO* 3.5 17.7 - - - +
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ALA* 4.4 7.6 - - + -
6B LEU 3.0 7.2 + - - +
7B ILE* 3.3 14.4 - - + +
8B ILE* 2.8 27.2 + - - +
104B THR* 4.4 8.5 - - + +
105B PRO* 1.3 79.7 - - - +
107B GLN* 1.3 63.1 + - - +
108B ILE* 5.2 0.4 - - + -
160B PRO* 3.9 16.8 - - + -
180B TRP* 3.6 30.7 - - + -
181B VAL* 4.3 14.1 - - + +
184B HIS* 4.0 22.0 - - + +
185B LEU* 3.6 36.6 - - + +
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE* 3.3 23.7 - - + +
10B THR* 3.6 12.2 - - + +
105B PRO* 5.8 0.7 - - + -
106B ILE* 1.3 75.3 - - - +
108B ILE* 1.3 71.7 + - - +
154B PRO* 3.6 15.2 - - - +
155B LEU* 2.8 57.7 + - - +
157B LEU* 4.3 8.6 - - + +
158B GLY 5.4 0.6 + - - -
160B PRO 3.0 15.7 + - - +
161B LEU* 3.2 18.0 - - + +
162B LEU 2.9 24.6 + - - -
180B TRP* 3.9 2.9 - - - -
195B GOL 4.2 7.9 + - - -
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.9 4.5 - - + -
8B ILE 2.8 11.9 + - - +
9B VAL* 3.3 6.6 - - + +
10B THR* 2.8 28.1 + - - +
20B LEU* 4.0 22.4 - - + -
24B LEU* 3.6 30.7 - - + -
106B ILE* 5.2 0.2 - - + -
107B GLN* 1.3 79.9 - - - +
109B ARG* 1.3 65.2 + - - +
110B CYS* 4.7 1.8 - - - -
162B LEU* 3.2 13.9 - - + +
164B VAL* 3.9 23.3 - - + -
177B ILE* 4.1 11.4 - - + -
180B TRP* 4.2 12.1 - - + -
181B VAL* 3.6 20.9 - - + -
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 3.5 12.8 - - + -
107B GLN 4.2 0.4 - - - -
108B ILE* 1.3 73.2 - - - +
110B CYS* 1.3 72.0 + - - +
111B VAL* 3.9 10.3 - - + +
151B ASP* 3.8 17.9 + - - +
152B ILE* 3.0 43.4 + - + -
153B PRO* 4.6 0.6 - - - +
154B PRO* 4.0 24.1 - - + +
161B LEU* 4.1 15.4 - - + +
162B LEU 2.8 8.5 + - - -
163B THR* 3.1 40.3 + - - +
164B VAL* 2.8 26.3 + - - +
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Residues in contact with CYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.3 7.0 - - - -
10B THR 2.8 14.3 + - - +
11B GLY* 3.4 16.8 - - - -
12B HIS 4.3 0.7 + - - -
15B THR* 3.4 33.1 + - - +
16B GLY 4.1 2.5 - - - -
17B LYS* 3.7 27.1 - - - +
20B LEU* 4.0 26.5 - - - -
108B ILE* 4.7 1.6 - - - -
109B ARG* 1.3 78.7 - - - +
111B VAL* 1.3 67.7 + - - +
152B ILE* 4.7 1.2 + - - +
164B VAL* 3.3 9.0 - - - +
166B THR* 5.0 2.0 - - + -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B THR* 3.9 8.5 - - - -
109B ARG* 3.9 21.3 - - - +
110B CYS* 1.3 81.0 - - - +
112B ALA* 1.3 64.3 + - - +
151B ASP* 3.4 46.2 - - + +
152B ILE 4.8 0.9 - - - +
163B THR* 3.7 18.2 - - + -
164B VAL 2.9 5.7 + - - +
165B ASP* 3.4 28.7 - - + +
166B THR* 2.9 27.7 + - - -
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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