Contacts of the helix formed by residues 120 - 137 (chain A) in PDB entry 1H41
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 SER 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A THR* 3.4 13.6 - - - +
97A GLY 5.0 0.4 + - - -
98A ALA* 2.6 34.0 + - - -
100A GLY 5.5 0.4 + - - -
118A ALA* 3.6 1.1 - - - +
119A ASN* 1.3 78.3 - - - +
121A ASP* 1.3 65.0 + - - +
122A VAL* 3.5 6.6 + - - +
123A GLY* 2.9 24.6 + - - -
124A VAL* 3.1 9.4 + - - +
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Residues in contact with ASP 121 (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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39A SER* 2.7 27.0 + - - -
41A THR* 3.5 25.5 - - + +
42A ILE* 3.5 20.2 - - + +
77A THR* 3.7 5.5 + - - +
80A ASN* 2.9 25.3 + - - -
120A SER* 1.3 73.5 - - - +
122A VAL* 1.3 63.2 + - - +
124A VAL* 3.0 6.7 + - - +
125A LEU 3.0 18.0 + - - -
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.7 10.6 - - + +
98A ALA 4.0 9.2 - - - +
99A GLU* 4.1 9.4 - - + +
120A SER* 3.3 11.9 + - - +
121A ASP* 1.3 77.9 - - - +
123A GLY* 1.3 59.4 + - - +
125A LEU* 3.1 11.7 + - + +
126A TYR* 2.9 70.7 + - + +
236A GLY* 3.8 24.5 - - - +
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Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU 3.6 22.4 - - - -
100A GLY 3.8 2.9 - - - -
101A TYR* 3.4 11.8 - - - +
118A ALA* 3.4 14.6 - - - -
120A SER* 2.9 20.6 + - - -
122A VAL* 1.3 77.0 - - - +
124A VAL* 1.3 56.5 + - - +
126A TYR* 3.4 0.8 + - - -
127A GLY 2.9 24.3 + - - -
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Residues in contact with VAL 124 (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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42A ILE* 3.9 20.2 - - + -
45A ALA* 4.5 2.5 - - + -
75A ILE* 3.9 35.7 - - + -
76A GLY* 3.5 33.9 - - - +
77A THR* 3.9 4.7 - - + -
116A VAL* 3.7 9.5 - - + +
118A ALA* 3.8 9.6 - - + +
120A SER 3.1 13.8 + - - +
121A ASP 3.0 8.6 + - - +
123A GLY* 1.3 74.8 - - - +
125A LEU* 1.3 58.1 + - - +
127A GLY 3.3 0.2 + - - -
128A SER* 2.8 34.9 + - - +
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Residues in contact with LEU 125 (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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41A THR* 4.1 6.5 - - + +
44A ALA* 4.3 5.6 - - + +
45A ALA* 3.8 36.7 - - + +
48A GLU* 5.4 0.9 - - + -
121A ASP 3.0 12.2 + - - +
122A VAL* 3.4 16.2 - - + +
124A VAL* 1.3 76.1 - - - +
126A TYR* 1.3 66.2 + - + +
128A SER* 3.2 3.6 + - - -
129A PHE* 3.1 52.3 + - + -
198A ALA* 4.1 10.5 - - + -
234A PRO 4.1 6.7 - - - +
235A TYR* 3.6 46.7 - - + +
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Residues in contact with TYR 126 (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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99A GLU* 3.5 25.7 + - + -
101A TYR* 4.0 5.4 - - + -
122A VAL* 2.9 52.3 + - + +
123A GLY 3.9 3.6 - - - +
125A LEU* 1.3 77.6 - - + +
127A GLY* 1.3 57.3 + - - +
129A PHE* 3.2 7.3 + - - +
130A HIS* 3.0 26.5 + - - +
155A ARG* 3.7 19.7 + - - -
198A ALA* 3.7 25.1 - - + -
201A GLY* 3.6 18.0 + - - -
202A ILE 4.3 0.9 + - - -
203A ASN* 3.6 27.0 - - - +
235A TYR 4.6 5.0 + - - -
236A GLY 4.2 4.2 + - - -
471A TRP* 3.6 24.2 - + + -
1725A EDO 4.0 10.0 - - - -
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Residues in contact with GLY 127 (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 TYR* 3.5 33.3 - - - -
103A LEU* 3.5 9.4 - - - +
116A VAL* 3.6 12.8 - - - -
123A GLY 2.9 13.8 + - - -
124A VAL 3.8 0.9 - - - -
126A TYR* 1.3 76.7 - - - +
128A SER* 1.3 57.6 + - - +
130A HIS* 3.2 1.2 + - - +
131A LEU* 2.8 25.6 + - - +
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Residues in contact with SER 128 (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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45A ALA* 3.8 16.1 - - - +
48A GLU* 5.8 2.7 - - - -
49A LEU* 3.4 36.0 - - - +
75A ILE* 4.2 0.7 - - - +
116A VAL* 3.7 9.8 - - - +
124A VAL* 2.8 28.8 + - - +
125A LEU* 3.2 7.4 + - - -
127A GLY* 1.3 73.7 - - - +
129A PHE* 1.3 59.3 + - - +
131A LEU* 3.3 5.7 + - - +
132A LEU* 3.0 35.0 + - - +
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Residues in contact with PHE 129 (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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12A LEU* 4.1 12.6 - - + -
14A TYR* 4.1 2.2 - - - -
48A GLU* 3.4 43.7 - - + -
125A LEU* 3.1 46.5 + - + -
126A TYR* 3.6 7.4 - - - +
128A SER* 1.3 79.2 - - - +
130A HIS* 1.3 57.3 + - - +
132A LEU* 3.3 6.6 + - + +
133A ARG* 2.9 30.7 + - - +
136A GLN* 4.8 0.5 - - - +
195A ARG* 3.6 21.5 - - - -
198A ALA* 3.7 15.3 - - + -
199A SER* 3.4 50.9 - - - +
235A TYR* 4.9 3.1 - + - -
1725A EDO 4.9 0.7 - - - -
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Residues in contact with HIS 130 (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 TYR* 2.7 34.8 + - + +
103A LEU* 3.8 5.2 - - + -
126A TYR 3.0 8.8 + - - +
127A GLY 3.2 7.6 + - - +
129A PHE* 1.3 72.6 - - - +
131A LEU* 1.3 66.5 + - - +
133A ARG* 3.0 26.7 + - + +
134A LEU* 2.9 35.0 + - + +
146A LEU* 3.5 25.1 - - + +
1715A EDO 3.3 26.4 + - - -
1725A EDO 3.8 6.5 - - - +
1726A EDO 2.8 26.3 + - - -
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Residues in contact with LEU 131 (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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30A ILE* 4.3 2.5 - - + -
49A LEU* 4.3 8.1 - - + -
53A LEU* 4.3 5.6 - - + -
73A LEU* 3.8 33.9 - - + -
103A LEU* 3.9 10.2 - - + +
114A VAL* 4.3 20.0 - - + -
116A VAL* 4.3 10.3 - - + -
127A GLY 2.8 16.2 + - - +
128A SER* 3.3 6.0 + - - +
130A HIS* 1.3 75.2 - - - +
132A LEU* 1.3 64.4 + - - +
134A LEU* 3.2 21.6 + - + +
135A ILE* 3.3 27.9 + - + +
141A LEU* 4.2 25.1 - - + -
144A LEU* 4.5 3.1 - - + -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A TYR* 3.6 23.8 - - + +
48A GLU* 3.8 26.9 - - + +
49A LEU* 3.7 19.5 - - + -
52A GLY* 3.8 7.6 - - - -
53A LEU* 3.8 35.9 - - + +
56A LEU* 4.0 10.3 - - + +
128A SER 3.0 22.3 + - - +
129A PHE* 3.7 8.5 - - + +
130A HIS 3.2 0.2 - - - -
131A LEU* 1.3 77.2 - - - +
133A ARG* 1.3 57.6 + - - +
135A ILE* 3.0 7.3 + - + +
136A GLN* 2.8 41.8 + - - +
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Residues in contact with ARG 133 (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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129A PHE 2.9 16.1 + - - +
130A HIS* 3.0 27.4 + - - +
132A LEU* 1.3 77.0 - - - +
134A LEU* 1.3 53.7 + - - +
136A GLN* 3.4 12.3 + - - +
137A THR* 2.7 41.7 + - + +
199A SER 3.8 8.1 + - - -
200A LEU* 5.9 0.6 - - - +
464A TYR* 3.2 25.1 + - - -
468A ARG* 3.6 16.8 - - - +
483A GLU* 3.9 5.8 + - - -
487A MET* 3.9 21.0 - - + +
1715A EDO 3.1 23.0 + - - -
1725A EDO 2.9 44.8 + - - -
1726A EDO 2.8 22.1 + - - +
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Residues in contact with LEU 134 (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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26A TYR* 3.6 0.2 + - - -
103A LEU* 3.9 20.4 - - + -
130A HIS* 2.9 19.6 + - + +
131A LEU* 3.4 10.5 - - + +
133A ARG* 1.3 74.5 - - - +
135A ILE* 1.3 60.8 + - - +
137A THR* 3.3 5.6 + - - -
138A GLN 3.1 3.1 + - - -
139A HIS* 2.8 47.1 + - + -
140A ALA 5.6 1.1 - - - +
141A LEU* 4.3 15.5 - - + -
144A LEU* 3.8 37.5 - - + -
146A LEU* 4.4 7.9 - - + -
1726A EDO 3.4 34.3 - - - +
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Residues in contact with ILE 135 (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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17A ILE* 3.3 17.1 - - + +
26A TYR* 3.7 41.1 + - + -
30A ILE* 4.1 11.9 - - + -
53A LEU* 3.7 29.6 - - + -
56A LEU* 3.9 27.1 - - + -
57A LEU* 4.2 8.3 - - + -
131A LEU* 3.3 22.6 + - + +
132A LEU* 3.0 8.1 + - - +
134A LEU* 1.3 75.2 - - - +
136A GLN* 1.3 64.6 + - - +
138A GLN* 3.0 12.5 + - - -
141A LEU* 4.5 9.4 - - + -
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Residues in contact with GLN 136 (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 TRP 2.8 29.3 + - - -
12A LEU* 4.0 8.2 - - - +
13A ARG 4.0 13.6 + - - +
14A TYR* 4.0 12.2 - - + -
17A ILE* 4.6 2.7 - - - +
56A LEU* 4.0 28.0 - - + -
129A PHE 4.8 0.7 - - - +
132A LEU* 2.8 38.2 + - - +
133A ARG* 3.4 10.6 + - - +
135A ILE* 1.3 72.9 - - - +
137A THR* 1.3 57.9 + - - +
138A GLN* 3.3 1.0 - - - +
486A ARG 4.0 7.1 - - - +
487A MET* 3.7 30.0 - - + +
491A ASN* 3.1 23.6 + - - -
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Residues in contact with THR 137 (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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133A ARG* 2.7 32.1 + - + +
134A LEU* 3.3 2.8 + - - -
136A GLN* 1.3 74.5 - - - +
138A GLN* 1.3 68.4 + - - +
139A HIS* 2.8 34.7 + - - -
483A GLU* 3.9 27.6 - - + +
486A ARG* 3.6 24.0 + - + +
487A MET* 3.9 22.9 - - + -
491A ASN* 3.6 8.3 - - - -
1726A EDO 4.3 2.6 - - - -
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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
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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