Contacts of the helix formed by residues 93 - 111 (chain A) in PDB entry 3LB2
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A SER 4.6 4.9 - - - +
92A LEU* 1.3 80.3 - - - +
94A THR* 1.3 65.7 + - - +
95A GLY* 3.6 10.0 + - - -
96A ASN* 2.8 33.8 + - - +
97A PHE* 3.6 7.1 - - - -
136A MET* 3.5 11.2 - - - -
137A LYS 3.9 20.2 - - - +
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Residues in contact with THR 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 74.0 - - - +
95A GLY* 1.3 58.5 + - - +
97A PHE* 3.0 9.1 + - - +
98A GLU* 2.9 32.6 + - - +
128A VAL* 3.8 27.0 - - - +
131A LEU* 4.0 10.8 - - + -
132A SER* 4.0 29.4 - - - +
136A MET* 3.6 24.0 - - + +
137A LYS 4.1 8.2 - - - +
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 3.1 9.8 + - - -
94A THR* 1.3 80.7 + - - +
96A ASN* 1.3 60.2 + - - +
98A GLU* 3.4 17.5 + - - +
99A LYS* 3.0 41.7 + - - +
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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
----------------------------------------------------------
24A PHE* 4.1 3.3 - - - -
31A GLU* 2.9 30.8 + - - -
34A TYR* 3.7 23.8 + - - -
92A LEU* 3.5 16.3 - - + +
93A THR* 2.8 39.7 + - - +
95A GLY* 1.3 75.4 - - - +
97A PHE* 1.3 64.6 + - + +
99A LYS* 3.5 6.3 + - - +
100A LEU* 3.2 17.7 + - - +
139A HEM 3.5 29.2 - - + +
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.6 9.0 - - + -
89A HIS* 4.0 18.6 - + - -
92A LEU* 3.9 18.2 - - + -
93A THR 3.6 12.3 - - - -
94A THR 3.0 7.4 + - - +
96A ASN* 1.3 76.5 - - + +
98A GLU* 1.3 65.6 + - - +
100A LEU* 3.2 3.0 + - + +
101A PHE* 3.0 36.6 + + + -
127A LEU* 5.1 0.7 - - + -
128A VAL* 4.3 6.7 - - + -
131A LEU* 3.5 26.5 - - + -
136A MET* 3.5 35.7 - - + -
139A HEM 3.3 61.2 - + + -
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 2.9 19.8 + - - +
95A GLY* 3.4 18.4 + - - +
97A PHE* 1.3 75.7 - - - +
99A LYS* 1.3 57.6 - - + +
101A PHE* 3.3 6.1 + - - +
102A VAL* 2.9 36.1 + - + +
128A VAL* 3.6 32.4 - - + +
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Residues in contact with LYS 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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24A PHE* 4.0 5.6 - - + -
28A TYR* 3.3 59.4 - - + +
31A GLU* 3.7 29.1 + - - +
95A GLY* 3.0 30.8 + - - +
96A ASN* 3.6 5.7 - - - +
97A PHE 3.2 0.2 - - - -
98A GLU* 1.3 74.9 - - + +
100A LEU* 1.3 66.5 + - - +
102A VAL* 3.3 1.4 + - - +
103A ALA* 3.0 20.4 + - - +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.7 6.3 - - + +
21A PHE* 5.3 1.3 - - - -
24A PHE* 3.5 36.5 - - + -
59A VAL* 5.6 0.2 - - + -
60A PHE* 4.6 16.4 - - + -
63A MET* 4.0 16.6 - - + -
96A ASN 3.2 14.0 + - - +
97A PHE* 3.2 7.8 + - + +
99A LYS* 1.3 76.4 - - - +
101A PHE* 1.3 63.3 + - + +
103A ALA* 3.3 1.9 + - - +
104A LEU* 2.9 30.2 + - + +
139A HEM 3.9 49.6 - - + -
191A BML 4.2 14.1 - - + -
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Residues in contact with PHE 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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63A MET* 4.0 29.2 - - + -
97A PHE* 3.0 33.7 + + + +
98A GLU* 3.9 4.9 - - - +
100A LEU* 1.3 78.2 - - + +
102A VAL* 1.3 63.9 + - - +
104A LEU* 3.7 17.2 - - + +
105A VAL* 2.9 32.2 + - + +
120A TRP* 4.1 12.3 - + - +
121A ASP* 5.7 1.6 - - - +
123A PHE* 3.8 35.9 - + - -
124A GLY* 3.7 29.8 - - - -
127A LEU* 3.9 24.2 - - + -
128A VAL* 5.5 1.1 - - + -
139A HEM 4.1 12.8 - - + -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 3.8 15.9 - - - -
28A TYR* 3.3 26.9 - - - +
98A GLU* 2.9 25.7 + - + +
99A LYS* 3.3 1.8 + - - +
101A PHE* 1.3 76.3 - - - +
103A ALA* 1.3 58.7 + - - +
105A VAL* 3.9 4.6 - - - +
106A GLU* 3.0 28.4 + - + +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 5.1 0.9 - - - +
23A ALA* 4.2 10.6 - - + +
24A PHE* 3.5 35.9 - - + +
27A LYS* 4.3 17.9 - - + -
28A TYR* 4.4 2.0 - - + -
99A LYS 3.0 16.1 + - - +
100A LEU 3.7 3.8 - - - +
102A VAL* 1.3 78.1 - - - +
104A LEU* 1.3 57.1 + - - +
106A GLU* 3.3 5.1 + - - +
107A TYR* 2.9 30.9 + - - +
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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
----------------------------------------------------------
9A ILE* 6.2 1.1 - - + -
20A ILE* 3.9 34.7 - - + +
60A PHE* 4.4 3.6 - - + -
63A MET* 3.7 36.3 - - + -
64A MET* 5.8 0.4 - - + -
100A LEU* 2.9 18.8 + - + +
101A PHE* 3.7 15.5 - - + +
102A VAL 3.3 0.2 - - - -
103A ALA* 1.3 76.0 - - - +
105A VAL* 1.3 60.7 + - + +
107A TYR* 3.3 4.3 + - - +
108A MET* 3.0 63.4 + - + +
120A TRP* 3.9 22.0 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 2.9 22.0 + - - +
102A VAL* 3.9 4.9 - - - +
104A LEU* 1.3 75.7 - - + +
106A GLU* 1.3 67.0 + - - +
108A MET* 3.2 6.7 + - - +
109A ARG* 3.0 59.2 + - - +
117A SER* 4.0 11.4 - - - +
120A TRP* 4.0 11.7 - - + +
121A ASP* 3.6 42.0 - - + +
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Residues in contact with GLU 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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23A ALA* 5.3 4.7 - - - +
27A LYS* 3.2 42.9 + - + +
102A VAL* 3.0 18.4 + - + +
103A ALA* 3.6 5.9 - - - +
105A VAL* 1.3 77.3 - - - +
107A TYR* 1.3 63.0 + - - +
109A ARG* 3.3 7.0 + - - +
110A ALA* 3.0 26.4 + - + +
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Residues in contact with TYR 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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16A TYR* 3.6 32.9 - + - -
19A ASP* 3.8 43.5 + - + +
20A ILE* 3.6 25.6 - - + -
23A ALA* 4.4 15.7 - - + -
103A ALA 2.9 17.4 + - - +
104A LEU* 3.4 8.7 - - - +
106A GLU* 1.3 76.3 + - - +
108A MET* 1.3 68.8 + - + +
110A ALA* 3.2 6.5 + - + +
111A SER* 3.0 29.0 + - - -
115A PHE* 4.7 10.3 - + - -
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Residues in contact with MET 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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9A ILE* 3.8 17.0 - - + -
20A ILE* 5.3 3.6 - - + -
104A LEU* 3.0 38.3 + - + +
105A VAL* 3.6 7.6 - - - +
107A TYR* 1.3 83.4 - - + +
109A ARG* 1.3 62.9 + - - +
111A SER* 2.7 22.2 + - - +
113A GLN 4.1 4.9 - - - -
115A PHE* 3.7 50.7 - - + +
117A SER* 4.4 9.6 - - - -
120A TRP* 3.4 50.9 - - + +
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Residues in contact with ARG 109 (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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105A VAL* 3.0 41.0 + - - +
106A GLU* 3.8 7.2 - - - +
108A MET* 1.3 77.7 - - - +
110A ALA* 1.3 59.4 + - - +
111A SER 3.6 5.4 + - - +
117A SER* 2.9 31.0 + - - +
118A GLN* 3.7 29.9 - - - +
121A ASP* 4.7 8.3 + - - +
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Residues in contact with ALA 110 (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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106A GLU* 3.0 21.6 + - + +
107A TYR* 3.8 5.8 - - + +
109A ARG* 1.3 73.6 - - - +
111A SER* 1.3 65.6 + - - +
112A GLY* 3.8 0.9 + - - -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 6.4 0.2 - - - -
107A TYR* 3.0 25.7 + - - -
108A MET 2.7 18.2 + - - +
109A ARG 3.8 7.1 - - - +
110A ALA* 1.3 82.0 - - - +
112A GLY* 1.3 61.5 + - - +
113A GLN 2.9 17.4 + - - -
115A PHE* 3.3 27.6 - - - -
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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