Contacts of the helix formed by residues 93 - 108 (chain A) in PDB entry 2B4J
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ILE* 5.0 0.4 - - - +
91A ALA* 3.0 22.1 + - + +
92A GLU* 1.3 79.0 - - - +
94A GLY* 1.3 63.7 + - - +
95A GLN* 3.7 8.1 + - - +
96A GLU* 3.3 26.4 + - - +
97A THR* 2.8 26.2 + - - -
120A ASN* 3.4 9.1 - - - +
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Residues in contact with GLY 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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93A THR* 1.3 72.5 - - - +
95A GLN* 1.3 57.3 + - - +
97A THR 3.3 0.2 + - - -
98A ALA* 2.8 32.6 + - - +
120A ASN* 3.5 23.9 - - - +
123A SER* 3.7 23.0 - - - -
125A THR* 3.7 6.5 - - - -
126A VAL* 3.5 2.8 - - - +
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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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93A THR* 3.3 9.1 + - - +
94A GLY* 1.3 74.7 - - - +
96A GLU* 1.3 65.7 + - + +
98A ALA* 3.6 3.8 - - - +
99A TYR* 2.9 41.5 + - + +
125A THR* 3.8 18.5 + - + +
171B HIS* 6.2 1.1 - - - -
173B LYS* 4.4 20.3 - - - +
174B THR* 4.5 3.6 + - - -
365D ILE 5.0 0.2 + - - -
366D ASP* 3.6 40.8 + - - +
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Residues in contact with GLU 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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74A LEU* 4.2 2.7 - - - +
89A ILE* 4.0 18.6 - - + +
90A PRO* 3.4 37.5 - - + +
91A ALA* 3.4 29.6 - - + +
93A THR* 3.3 11.3 + - - +
95A GLN* 1.3 84.6 - - + +
97A THR* 1.3 62.4 + - - +
99A TYR* 3.5 16.1 + - - +
100A PHE* 3.1 24.9 + - - +
173B LYS* 5.6 4.7 + - - -
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Residues in contact with THR 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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63A LEU* 4.3 10.5 - - + -
74A LEU* 3.8 15.0 - - + +
89A ILE* 4.8 3.3 - - - +
93A THR 2.8 17.7 + - - -
94A GLY 3.7 1.3 - - - -
96A GLU* 1.3 75.1 - - - +
98A ALA* 1.3 58.5 + - - +
100A PHE* 3.5 3.3 + - - +
101A LEU* 3.0 29.4 + - + +
120A ASN* 3.1 26.3 + - - -
121A PHE* 3.5 35.0 - - + -
126A VAL* 3.6 15.9 - - + -
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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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94A GLY 2.8 21.2 + - - +
95A GLN* 3.6 8.3 - - - +
97A THR* 1.3 74.9 - - - +
99A TYR* 1.3 55.7 + - - +
101A LEU* 3.3 4.5 + - - +
102A LEU* 2.9 36.2 + - + +
125A THR* 3.7 31.9 - - - +
126A VAL* 3.8 6.2 - - - +
129A ALA* 3.9 13.7 - - + +
365D ILE 5.9 0.7 - - - +
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Residues in contact with TYR 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* 2.9 28.2 + - + +
96A GLU* 3.8 18.4 - - - +
97A THR 3.3 0.2 - - - -
98A ALA* 1.3 71.6 - - - +
100A PHE* 1.3 66.8 + - - +
102A LEU* 3.4 10.3 + - + +
103A LYS* 3.1 51.3 + - + +
87B GLU* 3.1 31.3 + - - +
88B VAL 4.5 2.8 + - - -
173B LYS* 3.5 58.3 - - + +
174B THR* 4.8 5.8 - - - -
177B GLN* 3.7 17.1 + - + -
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Residues in contact with PHE 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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63A LEU* 4.7 9.6 - - + -
74A LEU* 3.4 47.8 - - + -
76A ALA* 3.7 31.6 - - + -
85A GLU* 4.1 23.8 - - + -
86A ALA* 4.4 3.8 - - - -
87A GLU* 4.3 31.4 - - + -
89A ILE* 5.2 4.0 - - + -
96A GLU 3.1 18.8 + - - +
97A THR 3.6 2.5 - - - +
99A TYR* 1.3 77.7 - - - +
101A LEU* 1.3 60.0 + - + +
103A LYS* 3.4 14.9 + - - +
104A LEU* 2.9 33.9 + - + +
107A ARG* 5.1 4.9 + - - -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.9 27.8 - - + -
97A THR* 3.0 17.1 + - + +
98A ALA* 3.7 5.8 - - - +
100A PHE* 1.3 74.3 - - + +
102A LEU* 1.3 62.3 + - - +
104A LEU* 3.6 17.0 - - + +
105A ALA* 2.9 31.9 + - - +
110A VAL* 4.5 1.3 - - + -
113A VAL* 3.8 31.9 - - + -
126A VAL* 4.0 17.9 - - + +
129A ALA* 5.3 3.8 - - + -
130A CYS* 3.8 28.9 - - - +
135A ILE* 4.0 14.8 - - + +
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Residues in contact with LEU 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* 2.9 23.1 + - + +
99A TYR* 3.4 11.2 + - + +
101A LEU* 1.3 77.7 - - - +
103A LYS* 1.3 61.6 + - - +
105A ALA* 4.0 4.5 - - - +
106A GLY* 3.4 16.6 + - - -
129A ALA* 4.0 30.1 - - + +
132A TRP* 4.2 20.2 - - + -
133A ALA* 4.4 6.7 - - + -
174B THR* 3.8 31.9 - - + +
177B GLN* 4.2 27.3 - - + +
178B MET* 5.0 3.8 - - + +
181B PHE* 4.9 3.4 - - + -
365D ILE* 4.0 15.5 - - + -
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Residues in contact with LYS 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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87A GLU* 3.7 24.7 + - - -
99A TYR* 3.1 40.1 + - + +
100A PHE* 3.6 14.8 - - - +
102A LEU* 1.3 76.3 - - - +
104A LEU* 1.3 63.8 + - - +
106A GLY* 3.3 9.8 + - - -
107A ARG* 3.5 39.2 + - - +
87B GLU* 3.1 31.9 + - + +
103B LYS* 4.6 2.4 - - - +
177B GLN* 3.4 39.7 - - + +
180B VAL* 6.0 0.9 - - - +
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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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61A TRP* 3.9 32.8 - - + -
63A LEU* 4.6 3.8 - - + -
76A ALA* 4.1 14.1 - - + -
85A GLU* 3.7 35.0 - - + +
100A PHE* 2.9 22.9 + - + +
101A LEU* 3.6 20.4 - - + +
103A LYS* 1.3 77.0 - - - +
105A ALA* 1.3 61.9 + - - +
107A ARG* 3.1 21.6 + - - +
108A TRP* 3.1 27.8 + - + +
110A VAL* 3.8 19.1 - - + +
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Residues in contact with ALA 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 LEU 2.9 17.6 + - - +
102A LEU 4.0 4.9 - - - +
104A LEU* 1.3 78.1 - - - +
106A GLY* 1.3 57.6 + - - +
108A TRP 2.8 16.6 - - - +
110A VAL* 3.8 15.7 + - + +
133A ALA* 4.0 8.3 - - + +
135A ILE* 4.0 22.4 - - + -
181B PHE* 3.5 18.6 - - + -
185B LYS* 3.1 14.9 + - - -
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Residues in contact with GLY 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 LEU 3.4 7.6 + - - -
103A LYS 3.3 6.3 + - - -
104A LEU 3.3 1.2 - - - -
105A ALA* 1.3 77.9 - - - +
107A ARG* 1.3 61.1 + - - +
83B TYR* 4.1 0.3 - - - -
177B GLN 5.5 0.4 - - - -
180B VAL* 4.9 5.6 - - - -
181B PHE* 3.6 30.4 - - - -
184B ASN* 3.0 32.9 + - - +
185B LYS* 4.2 5.5 + - - -
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Residues in contact with ARG 107 (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 GLU* 2.5 26.9 + - - -
100A PHE* 5.1 5.9 + - - -
103A LYS* 3.5 34.3 + - - +
104A LEU* 3.1 23.6 + - - +
106A GLY* 1.3 82.2 - - - +
108A TRP* 1.3 75.8 + - + +
83B TYR* 3.0 27.8 - - - +
85B GLU* 2.9 34.7 + - + +
107B ARG* 3.0 40.6 - - - +
108B TRP* 3.9 6.5 - - + -
180B VAL* 6.0 2.2 - - + -
184B ASN* 5.6 0.2 - - - +
185B LYS* 4.5 2.2 - - - -
197B GLY* 5.5 5.1 - - - +
201B VAL* 5.8 0.5 - - - +
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Residues in contact with TRP 108 (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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61A TRP* 3.6 31.2 - + + -
83A TYR* 3.4 30.6 + + - -
85A GLU* 2.9 24.1 + - - -
104A LEU* 3.1 16.7 + - + +
105A ALA 2.8 12.3 - - - +
107A ARG* 1.3 91.1 - - + +
109A PRO* 1.4 78.8 - - + +
110A VAL* 3.2 6.5 + - + -
200A ILE* 3.9 36.6 - - + -
201A VAL* 4.3 6.1 - - + -
204A ILE* 4.7 3.1 - - + -
107B ARG* 3.9 18.1 - - + +
108B TRP* 3.6 32.5 - + - -
185B LYS* 2.8 19.0 + - - +
201B VAL* 4.1 15.7 - - + -
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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
------------------------------------------------------------
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