Contacts of the helix formed by residues 99 - 117 (chain A) in PDB entry 3H4B
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 LEU 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 3.7 17.9 - - + +
59A GLN* 3.5 14.6 - - - +
96A GLY 3.5 22.0 - - - +
97A GLU 3.7 0.6 + - - -
98A ASP* 1.3 71.3 + - - +
100A THR* 1.3 56.7 + - - +
101A ARG 3.5 0.9 - - - -
102A TYR* 3.9 13.2 - - + -
103A ARG* 3.0 39.1 + - - +
125A PHE* 4.0 22.0 - - + -
841T G 3.2 36.8 - - - +
842T G 3.3 34.4 + - - +
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Residues in contact with THR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP* 2.8 29.1 + - - -
99A LEU* 1.3 77.3 - - - +
101A ARG* 1.3 65.6 + - + +
103A ARG* 3.7 22.6 + - - +
104A GLU* 3.0 55.6 + - + +
304A GLU* 5.4 2.1 + - - -
331A ARG* 5.4 1.2 - - - -
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.3 15.6 - - + +
43A GLU* 2.7 43.9 + - - -
46A SER* 2.6 32.1 + - - -
98A ASP 4.6 2.9 + - - +
99A LEU 3.5 0.2 - - - -
100A THR* 1.3 82.2 - - + +
102A TYR* 1.3 65.2 + - + +
104A GLU* 3.3 13.1 + - - +
105A MET* 2.9 31.6 + - - +
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 3.3 17.4 - - + -
39A TYR* 3.4 72.7 - + + -
42A VAL* 3.8 22.9 - - + -
43A GLU* 2.4 35.6 + - - +
57A VAL* 3.7 4.5 - - - +
95A ASN 4.1 0.2 + - - -
96A GLY* 3.5 29.1 - - - -
98A ASP 3.9 13.2 - - - -
99A LEU* 3.9 18.2 - - + +
100A THR 3.3 0.4 - - - -
101A ARG* 1.3 79.4 - - + +
103A ARG* 1.3 53.9 + - - +
105A MET* 3.1 2.5 + - - -
106A SER* 2.7 31.4 + - - -
125A PHE* 4.3 4.7 - - + -
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP* 5.3 0.6 + - - -
99A LEU* 3.0 34.2 + - - +
100A THR* 3.7 25.0 + - - +
102A TYR* 1.3 76.9 - - - +
104A GLU* 1.3 67.6 + - - +
106A SER* 3.0 14.1 + - - -
107A TYR* 3.1 39.6 + - + -
125A PHE* 3.7 29.3 - - + -
299A PRO* 6.5 0.2 - - - -
304A GLU* 4.2 5.5 + - - -
331A ARG* 3.0 57.7 - - - +
842T G 4.5 9.9 + - - -
843T G 4.0 8.7 + - - -
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 3.0 38.0 + - + +
101A ARG* 3.6 13.5 - - - +
102A TYR 3.3 0.2 - - - -
103A ARG* 1.3 85.2 + - + +
105A MET* 1.3 61.5 + - + +
107A TYR* 3.5 7.0 + - - +
108A LYS* 3.3 31.9 + - - +
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Residues in contact with MET 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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38A PHE* 3.8 13.5 - - + -
42A VAL* 4.4 18.8 - - + -
45A ILE* 6.1 4.3 - - + -
101A ARG 2.9 17.0 + - - +
102A TYR 3.6 4.0 - - - +
104A GLU* 1.3 75.7 - - + +
106A SER* 1.3 66.3 + - - +
108A LYS* 3.1 30.3 + - + +
109A VAL* 3.0 23.0 + - - +
191A LEU* 4.5 17.9 - - + +
193A LEU* 3.7 31.9 - - + -
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Residues in contact with SER 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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38A PHE* 3.6 5.6 - - - -
102A TYR 2.7 13.8 + - - -
103A ARG* 3.0 12.5 + - - -
105A MET* 1.3 77.6 - - - +
107A TYR* 1.3 56.4 + - - +
109A VAL* 3.4 7.5 + - - +
110A THR* 2.9 28.2 + - - -
122A ARG* 2.4 28.0 + - - -
125A PHE* 2.4 47.3 + - - +
128A ASN* 5.0 1.6 + - - -
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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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103A ARG* 3.1 44.8 + - + -
104A GLU* 4.1 7.4 - - - +
106A SER* 1.3 71.7 - - - +
108A LYS* 1.3 61.3 + - + +
109A VAL 3.1 1.6 - - - -
110A THR* 3.7 6.8 - - + -
111A GLU* 2.9 48.4 + - + +
122A ARG* 3.4 44.1 + - - +
125A PHE* 6.0 0.9 - + - -
297A GLY 4.4 12.2 + - - -
298A PRO* 5.5 0.7 - - + -
299A PRO* 3.0 37.4 - - + +
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Residues in contact with LYS 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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104A GLU* 3.3 19.7 + - - +
105A MET* 3.1 30.0 + - + +
107A TYR* 1.3 78.6 - - + +
109A VAL* 1.3 62.6 + - - +
111A GLU* 3.8 10.5 - - - +
112A LEU* 3.2 23.6 + - - +
191A LEU* 3.7 30.9 - - + +
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Residues in contact with VAL 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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33A VAL* 5.4 0.2 - - + -
35A LEU* 4.0 18.6 - - + -
38A PHE* 4.9 0.4 - - + -
105A MET 3.0 14.1 + - - +
106A SER* 3.6 9.4 - - - +
108A LYS* 1.3 75.0 - - - +
110A THR* 1.3 67.3 + - - +
112A LEU* 3.4 4.8 + - - +
113A LEU* 3.1 24.7 + - + +
125A PHE 6.1 0.2 - - - +
128A ASN* 3.9 18.2 - - - +
187A MET* 3.9 27.1 - - + -
191A LEU* 4.0 11.4 - - + -
193A LEU* 3.5 30.1 - - + -
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Residues in contact with THR 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 SER 2.9 16.7 + - - -
107A TYR* 3.4 9.2 + - + -
109A VAL* 1.3 78.4 - - - +
111A GLU* 1.3 57.8 + - - +
113A LEU* 3.1 6.2 + - - +
114A GLU* 2.9 44.4 + - - +
120A VAL* 3.8 15.5 - - + +
122A ARG* 3.1 33.2 + - + +
128A ASN* 3.1 27.9 + - - +
296A SER* 5.7 1.1 - - - -
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Residues in contact with GLU 111 (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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107A TYR* 2.9 37.3 + - + +
108A LYS* 3.8 9.5 + - - +
110A THR* 1.3 73.3 - - - +
112A LEU* 1.3 63.9 + - - +
114A GLU* 2.9 33.2 + - - +
115A GLU* 3.1 10.9 + - - +
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Residues in contact with LEU 112 (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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108A LYS 3.2 13.4 + - - +
109A VAL 3.6 3.8 - - - +
111A GLU* 1.3 78.7 - - - +
113A LEU* 1.3 75.2 + - + +
115A GLU* 3.1 28.4 + - - +
116A PHE* 3.4 29.5 - - + -
183A MET 4.5 0.4 - - - +
186A ALA* 3.8 19.7 - - + +
187A MET* 3.8 33.0 - - + -
190A GLN* 4.3 16.8 - - + +
191A LEU* 3.8 18.6 - - + -
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Residues in contact with LEU 113 (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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33A VAL* 4.0 17.9 - - + -
109A VAL* 3.1 20.9 + - + +
110A THR 3.1 8.0 + - - +
112A LEU* 1.3 86.3 - - + +
114A GLU* 1.3 61.8 + - - +
115A GLU 3.2 0.7 + - - -
116A PHE* 3.3 15.4 + - - +
117A SER 3.3 12.8 + - - +
120A VAL* 3.8 6.1 - - + +
128A ASN* 3.5 39.3 - - + +
130A VAL* 4.2 13.9 - - + -
183A MET* 3.7 43.8 - - + +
187A MET* 4.3 10.8 - - + -
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Residues in contact with GLU 114 (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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110A THR* 2.9 26.4 + - - +
111A GLU* 2.9 33.6 + - - +
113A LEU* 1.3 75.1 - - - +
115A GLU* 1.3 64.4 + - - +
117A SER 3.2 23.0 - - - -
118A PRO* 3.2 19.5 - - + +
120A VAL* 3.7 19.7 - - + +
295A LEU* 4.7 12.3 - - - +
297A GLY* 4.8 9.5 + - - -
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Residues in contact with GLU 115 (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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111A GLU 3.1 8.4 + - - +
112A LEU* 3.1 20.1 - - - +
114A GLU* 1.3 77.9 - - - +
116A PHE* 1.3 70.5 + - + +
117A SER* 4.3 0.2 - - - -
118A PRO* 5.3 0.9 - - - +
190A GLN* 5.1 7.3 + - - +
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Residues in contact with PHE 116 (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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112A LEU* 3.4 37.5 - - + -
113A LEU* 3.3 10.6 + - - +
115A GLU* 1.3 83.3 - - + +
117A SER* 1.3 61.9 + - - +
118A PRO* 4.7 0.7 - - - +
135A MET* 3.7 37.6 - - + +
139A ARG* 5.2 0.2 - - - -
179A ILE* 4.5 2.7 - - + -
182A GLU* 3.9 28.3 - - + -
183A MET* 3.5 52.0 - - + -
186A ALA* 4.1 9.4 - - + -
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Residues in contact with SER 117 (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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113A LEU 3.3 4.5 + - - +
114A GLU 3.2 3.9 - - - +
116A PHE* 1.3 84.1 + - - +
118A PRO* 1.3 77.7 - - - +
119A VAL* 3.2 5.2 + - - +
120A VAL* 3.2 20.8 - - - +
130A VAL* 3.9 20.0 - - - -
131A ASP 3.5 16.3 + - - -
132A LEU* 4.9 1.8 - - - -
134A GLU* 5.6 4.2 - - - +
135A MET* 4.8 16.0 + - - +
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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
------------------------------------------------------------
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