Contacts of the helix formed by residues 93 - 106 (chain A) in PDB entry 183L
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 ALA 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ASP* 1.3 74.0 - - - +
94A VAL* 1.3 64.5 + - + +
96A ARG* 3.4 7.7 + - - +
97A ALA* 3.3 8.1 + - - +
170A HED 2.3 52.3 + - + -
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Residues in contact with VAL 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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92A ASP* 3.1 5.8 + - - +
93A ALA* 1.3 77.4 - - + +
95A ARG* 1.3 65.0 + - - +
97A ALA* 3.0 15.1 + - - +
98A ALA 3.3 7.4 + - - -
152A THR* 3.9 14.9 - - + +
156A GLY 3.5 34.8 - - - +
157A THR* 3.8 16.8 - - - +
158A TRP* 3.8 36.8 - - + +
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Residues in contact with ARG 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 LEU* 4.3 12.6 - - + -
92A ASP* 3.0 38.4 + - - +
94A VAL* 1.3 78.0 - - - +
96A ARG* 1.4 59.8 + - - +
98A ALA* 3.0 16.6 + - - +
99A ALA* 3.0 11.6 + - - +
126A TRP* 3.5 51.7 - - - +
152A THR 3.9 13.5 - - - +
153A PHE* 2.5 47.5 + - + +
154A ARG 3.2 16.8 + - - -
155A THR 3.3 4.6 + - - -
156A GLY* 3.2 23.5 - - - +
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Residues in contact with ARG 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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88A TYR* 3.0 58.1 + - + +
89A ASP* 3.0 34.9 + - - +
91A LEU* 3.1 19.5 + - + +
92A ASP 3.1 15.4 + - - +
93A ALA* 3.7 10.4 - - - +
94A VAL 3.2 0.2 - - - -
95A ARG* 1.4 70.8 - - - +
97A ALA* 1.4 66.8 + - - +
99A ALA* 3.1 7.6 + - - +
100A ILE* 3.0 26.9 + - - +
170A HED 4.3 19.3 - - - +
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Residues in contact with ALA 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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3A ILE* 3.4 25.8 - - + +
6A MET* 4.2 7.4 - - - -
93A ALA 3.3 6.4 + - - +
94A VAL 3.0 8.2 + - - +
96A ARG* 1.4 76.5 - - - +
98A ALA* 1.3 63.4 + - - +
100A ILE* 3.1 8.3 + - - -
101A ASN* 3.1 19.2 + - - +
158A TRP* 3.4 35.4 - - + -
170A HED 4.0 7.5 + - - +
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Residues in contact with ALA 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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6A MET* 4.1 11.7 - - + +
94A VAL 3.3 2.6 + - - -
95A ARG 3.0 10.9 + - - +
97A ALA* 1.3 78.6 - - - +
99A ALA* 1.3 59.8 + - - +
101A ASN* 3.4 4.4 - - - +
102A MET* 3.3 26.3 + - - +
149A VAL* 3.9 12.8 - - + +
152A THR* 3.8 24.0 - - + -
153A PHE* 3.6 25.4 - - + -
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Residues in contact with ALA 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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78A ILE* 4.0 2.4 - - - +
88A TYR* 4.1 10.3 - - + -
91A LEU* 4.3 2.7 - - + -
95A ARG 3.0 11.2 + - - +
96A ARG* 3.1 9.2 + - - +
98A ALA* 1.3 77.2 - - - +
100A ILE* 1.3 58.8 + - - +
102A MET 3.6 0.5 + - - -
103A VAL* 3.4 19.4 + - - +
153A PHE* 3.5 10.4 - - + -
400A DEN 3.5 54.1 - - + -
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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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3A ILE* 4.0 27.8 - - + -
7A LEU* 4.8 5.4 - - + -
71A VAL* 4.8 5.4 - - + +
74A ALA* 4.0 22.2 - - + -
75A VAL* 3.9 22.7 - - + -
78A ILE* 3.9 20.6 - - + -
88A TYR* 3.9 17.7 - - + +
96A ARG 3.0 20.9 + - - +
97A ALA* 3.1 4.2 + - - +
99A ALA* 1.3 72.6 - - - +
101A ASN* 1.3 57.6 + - - +
103A VAL* 3.2 1.7 + - - +
104A PHE* 2.7 35.6 + - + +
170A HED 4.0 20.6 - - + -
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Residues in contact with ASN 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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3A ILE* 4.1 2.1 - - - +
6A MET* 3.5 24.9 - - - +
7A LEU* 3.8 18.7 - - + +
10A ASP* 2.8 27.6 + - - -
97A ALA 3.1 11.5 + - - +
98A ALA 3.4 11.0 - - - +
100A ILE* 1.3 76.9 - - - +
102A MET* 1.3 65.1 + - - +
104A PHE* 3.3 2.3 + - - +
105A GLN* 2.9 21.5 + - - +
145A ARG* 2.6 33.1 + - - -
149A VAL* 3.8 13.6 - - + +
161A TYR* 3.6 4.2 + - - -
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Residues in contact with MET 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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98A ALA 3.3 11.0 + - - +
99A ALA 3.9 7.0 - - - +
100A ILE 3.2 0.4 - - - -
101A ASN* 1.3 79.7 - - - +
103A VAL* 1.4 55.8 + - - +
105A GLN* 3.2 4.7 + - - +
106A MET* 2.9 62.9 + - + +
111A VAL* 4.1 5.2 - - + -
114A PHE* 4.0 31.2 - - + -
133A LEU* 4.4 6.3 - - + -
138A TRP* 3.9 24.7 - - + -
149A VAL* 3.9 11.9 - - + -
153A PHE* 3.7 18.4 - - - -
400A DEN 3.7 29.8 - - + -
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Residues in contact with VAL 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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74A ALA* 4.2 26.5 - - + +
77A GLY* 6.1 0.2 - - - -
78A ILE* 4.0 21.5 - - + -
84A LEU* 4.5 8.1 - - + -
99A ALA 3.4 11.7 + - - +
100A ILE* 3.2 6.5 + - - +
102A MET* 1.4 72.9 - - - +
104A PHE* 1.3 61.5 + - - +
107A GLY* 2.6 33.9 + - - +
108A GLU* 4.1 19.7 - - + +
111A VAL* 4.1 20.0 - - + -
400A DEN 4.4 8.5 - - + -
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Residues in contact with PHE 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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7A LEU* 3.6 28.0 - - + -
11A GLU* 3.9 24.5 - - + -
29A ILE 3.4 26.2 - - - -
30A GLY 4.1 14.3 - - - +
67A PHE* 4.0 24.0 - + - -
70A ASP* 3.6 40.6 - - + -
71A VAL* 4.1 7.4 - - + -
74A ALA* 4.7 8.5 - - + +
100A ILE* 2.7 23.1 + - + +
101A ASN 3.5 4.3 - - - +
103A VAL* 1.3 75.3 - - - +
105A GLN* 1.3 62.4 + - - +
107A GLY 4.5 1.0 + - - -
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Residues in contact with GLN 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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11A GLU* 4.3 4.0 - - - +
21A THR* 5.5 1.4 + - - -
101A ASN* 2.9 18.3 + - - +
102A MET* 3.7 4.4 - - - +
104A PHE* 1.3 82.3 - - - +
106A MET* 1.3 62.7 + - + +
138A TRP* 2.9 32.7 + - - -
142A THR* 3.4 30.7 + - - +
145A ARG* 3.4 41.3 + - - +
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Residues in contact with MET 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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102A MET* 2.9 45.5 + - + +
105A GLN* 1.3 84.9 - - + +
107A GLY* 1.3 65.9 + - - +
109A THR* 5.1 1.0 - - - +
110A GLY* 3.2 31.0 + - - +
111A VAL* 3.3 21.1 - - + -
114A PHE* 4.1 10.5 - - - -
138A TRP* 3.3 48.0 - - + +
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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