Contacts of the helix formed by residues 86 - 101 (chain A) 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 ARG 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE* 6.3 2.9 - - - -
84A ASN* 4.0 9.6 - - - +
85A PHE* 1.3 74.6 - - - +
87A VAL* 1.3 61.1 + - - +
88A ASP* 2.7 41.4 + - - +
89A LEU* 3.9 22.2 - - + +
90A ASP* 2.8 45.0 + - - +
93A ARG* 6.0 1.3 - - - +
155A LEU* 3.9 2.5 - - - -
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Residues in contact with VAL 87 (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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85A PHE 4.1 1.2 + - - -
86A ARG* 1.3 71.7 - - - +
88A ASP* 1.3 65.2 + - + +
89A LEU 3.2 1.4 + - - -
91A THR* 2.6 37.0 + - - +
153A PRO* 3.8 29.5 - - + +
154A PRO 3.4 26.7 - - - +
155A LEU* 3.9 5.1 - - + +
156A PRO* 4.2 14.1 - - + -
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Residues in contact with ASP 88 (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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86A ARG* 2.7 48.2 + - - +
87A VAL* 1.3 81.7 - - + +
89A LEU* 1.3 80.1 + - - +
91A THR* 4.9 0.9 - - - -
92A GLU* 5.5 4.0 + - - +
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Residues in contact with LEU 89 (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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86A ARG* 3.3 27.5 + - + +
88A ASP* 1.3 97.9 + - - +
90A ASP* 1.3 64.1 + - - +
91A THR 3.3 2.0 + - - -
92A GLU* 3.6 7.9 + - - +
93A ARG* 3.3 56.0 + - - +
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Residues in contact with ASP 90 (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 ILE* 4.2 7.9 - - - +
66A TYR* 2.6 30.8 + - - +
85A PHE* 3.5 20.5 - - + -
86A ARG* 2.8 42.8 + - - +
89A LEU* 1.3 70.5 - - - +
91A THR* 1.3 64.9 + - - +
93A ARG* 3.0 25.5 + - - -
94A MSE 3.0 30.5 + - - +
155A LEU* 4.0 15.5 - - + -
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Residues in contact with THR 91 (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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86A ARG 4.0 0.4 + - - -
87A VAL* 2.6 28.1 + - - +
88A ASP 5.5 0.2 - - - -
89A LEU 3.3 1.0 - - - -
90A ASP* 1.3 78.5 - - - +
92A GLU* 1.3 62.6 + - - +
94A MSE 3.4 4.4 + - - +
95A GLN* 3.1 45.5 + - + +
155A LEU* 4.3 2.6 - - - +
156A PRO* 3.4 45.5 - - + +
157A LEU* 4.7 7.7 - - + +
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Residues in contact with GLU 92 (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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88A ASP 5.5 3.0 + - - +
89A LEU* 3.6 10.0 + - - +
91A THR* 1.3 79.7 - - - +
93A ARG* 1.3 56.9 + - + +
95A GLN* 3.3 16.1 + - - +
96A ASN* 2.9 47.8 + - - +
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Residues in contact with ARG 93 (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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59A ALA* 5.9 3.2 + - - +
62A ILE* 3.6 25.9 - - - +
63A MSE 6.2 2.5 - - - +
66A TYR* 3.4 35.9 - - + +
86A ARG* 5.9 1.6 - - - +
89A LEU* 3.3 49.4 + - - +
90A ASP* 3.0 34.2 + - - +
91A THR 3.4 0.6 - - - -
92A GLU* 1.3 77.5 - - + +
94A MSE 1.3 57.2 + - - +
96A ASN* 3.5 10.1 + - - +
97A LEU* 2.9 28.2 + - - +
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Residues in contact with MSE 94 (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 LEU* 3.7 25.4 - - - -
8A ILE* 4.1 24.9 - - + -
66A TYR* 3.5 23.8 - - + +
81A MSE 3.8 27.1 - - + -
85A PHE* 3.9 12.8 - - + -
90A ASP 3.0 25.7 + - - +
91A THR 3.7 0.7 - - - +
93A ARG* 1.3 73.6 - - - +
95A GLN* 1.3 60.7 + - - +
97A LEU* 3.4 3.6 + - - +
98A HIS* 2.9 22.2 + - - +
103A PHE* 3.5 18.7 - - + -
155A LEU* 4.2 10.3 - - + -
157A LEU* 3.6 27.1 - - + -
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Residues in contact with GLN 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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91A THR* 3.1 35.4 + - + +
92A GLU* 3.5 16.8 - - - +
94A MSE 1.3 73.8 - - + +
96A ASN* 1.3 67.9 + - - +
98A HIS* 3.2 7.9 + - - +
99A THR* 3.1 26.5 + - - -
157A LEU* 5.7 4.0 - - + -
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Residues in contact with ASN 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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92A GLU* 2.9 42.6 + - - +
93A ARG* 3.7 10.0 - - - +
95A GLN* 1.3 77.6 - - - +
97A LEU* 1.3 62.4 + - - +
99A THR* 3.3 16.6 + - - -
100A ILE* 3.3 19.2 + - - +
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Residues in contact with LEU 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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6A LEU* 3.9 27.6 - - + -
66A TYR* 3.9 30.7 - - + +
69A ALA* 4.1 10.1 - - + -
70A ALA* 3.7 40.2 - - + +
73A LEU* 4.0 13.7 - - + -
81A MSE 4.5 0.9 - - - -
93A ARG 2.9 18.3 + - - +
94A MSE 3.5 7.0 - - - +
95A GLN 3.2 0.2 - - - -
96A ASN* 1.3 75.8 - - - +
98A HIS* 1.3 53.0 + - - +
100A ILE* 3.2 11.0 + - + +
101A ALA* 2.7 39.1 + - + +
103A PHE* 4.0 5.6 - - + -
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Residues in contact with HIS 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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3A THR* 5.9 0.4 - - - +
94A MSE 2.9 14.5 + - - +
95A GLN* 3.2 11.8 + - - +
97A LEU* 1.3 77.0 - - - +
99A THR* 1.3 64.6 + - - +
101A ALA 3.7 2.5 - - - -
102A PRO* 3.1 33.0 - - + +
103A PHE* 3.2 58.8 + + + -
105A PRO* 5.7 1.1 - - + -
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Residues in contact with THR 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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95A GLN 3.1 13.9 + - - -
96A ASN* 3.5 13.3 + - - -
97A LEU 3.2 0.4 - - - -
98A HIS* 1.3 81.4 + - - +
100A ILE* 1.3 65.3 + - + +
102A PRO* 4.4 4.9 - - - +
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Residues in contact with ILE 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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70A ALA* 3.9 24.0 - - + -
74A GLN* 3.0 29.2 + - - +
96A ASN 3.3 12.3 + - - +
97A LEU* 3.4 15.3 - - + +
99A THR* 1.3 85.3 - - + +
101A ALA* 1.3 63.0 + - + +
102A PRO* 3.8 4.6 - - - +
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Residues in contact with ALA 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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70A ALA* 3.8 20.6 - - - +
73A LEU* 3.9 15.4 - - + +
74A GLN* 3.8 20.6 - - + +
97A LEU* 2.7 22.8 + - + +
98A HIS 3.4 2.7 - - - -
100A ILE* 1.3 80.5 - - + +
102A PRO* 1.3 71.8 - - - +
103A PHE* 3.3 14.7 - - - -
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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