Contacts of the helix formed by residues 123 - 137 (chain A) in PDB entry 1H1W
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 LYS 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.4 53.7 - - + -
118A ILE* 2.8 26.1 + - + +
121A GLU* 3.4 21.3 + - + +
122A ASN* 1.3 73.3 + - - +
124A VAL* 1.3 65.6 + - - +
125A PRO* 3.2 3.1 - - - -
126A TYR* 3.0 33.9 + - + +
127A VAL* 3.0 27.3 + - + +
1366A GOL 6.1 1.1 - - - -
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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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118A ILE* 3.6 18.1 - - + +
119A ILE* 4.3 24.7 - - + -
122A ASN* 3.4 2.0 - - - -
123A LYS* 1.3 78.2 - - - +
125A PRO* 1.3 69.0 - - + +
127A VAL* 4.2 2.1 - - - +
128A THR* 2.7 41.9 + - - +
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Residues in contact with PRO 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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122A ASN* 3.8 13.7 - - + +
123A LYS 3.3 4.0 - - - -
124A VAL* 1.3 97.3 - - + +
126A TYR* 1.3 64.1 - - + +
128A THR* 3.8 4.7 - - - -
129A ARG* 3.0 42.0 + - - +
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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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122A ASN 4.3 7.0 - - - -
123A LYS* 3.0 48.0 + - + +
125A PRO* 1.3 82.6 - - + +
127A VAL* 1.3 61.1 + - - +
129A ARG* 3.3 18.6 + - - -
130A GLU 2.9 24.3 + - - -
225A GLY* 3.4 30.7 - - - +
226A THR* 4.0 21.3 - - + -
241A SEP 3.8 29.5 + - - -
242A PHE* 4.6 12.8 - + + +
1366A GOL 4.0 16.4 - - - +
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Residues in contact with VAL 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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93A PHE* 5.8 1.1 - - + -
113A LEU* 3.9 17.9 - - + -
118A ILE* 3.5 31.0 - - + -
123A LYS* 3.0 18.8 + - + +
124A VAL* 4.2 2.7 - - - +
126A TYR* 1.3 75.8 - - - +
128A THR* 1.3 63.1 + - - +
130A GLU* 3.4 5.4 + - - +
131A ARG* 3.2 20.6 + - - +
155A LEU* 3.8 21.1 - - + -
157A PHE* 3.7 24.4 - - + -
1366A GOL 4.2 13.7 - - - -
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Residues in contact with THR 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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124A VAL* 2.7 33.9 + - - +
125A PRO* 3.8 6.1 - - - -
127A VAL* 1.3 78.4 - - - +
129A ARG* 1.3 56.5 + - - +
131A ARG* 3.4 6.8 + - - +
132A ASP* 3.0 50.6 + - - +
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Residues in contact with ARG 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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125A PRO* 3.0 31.2 + - - +
126A TYR* 3.3 19.2 + - - +
128A THR* 1.3 74.7 - - - +
130A GLU* 1.3 57.8 + - - +
132A ASP* 4.4 5.6 - - - -
133A VAL* 2.8 53.7 + - + +
204A ARG* 3.3 7.2 - - - +
224A PHE 4.1 1.3 - - - +
225A GLY 3.1 21.3 + - - +
226A THR* 3.8 0.4 - - - +
227A ALA 2.8 35.4 + - - +
228A LYS* 4.8 8.6 - - - +
229A VAL* 4.8 9.0 - - + +
241A SEP 3.0 31.4 + - - -
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Residues in contact with GLU 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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111A LYS* 2.7 32.5 + - - +
113A LEU* 4.5 1.2 - - - +
126A TYR 2.9 8.6 + - - +
127A VAL* 3.5 8.8 - - - +
129A ARG* 1.3 75.6 - - - +
131A ARG* 1.3 62.8 + - - +
133A VAL* 4.1 0.7 - - - +
134A MET* 3.0 49.7 + - + +
157A PHE* 3.9 20.6 - - + -
159A LEU* 5.7 0.9 - - - +
222A THR* 5.4 0.7 + - - -
223A ASP* 4.7 2.8 + - - -
224A PHE* 4.0 12.6 + - - +
225A GLY* 3.5 27.5 - - - +
1366A GOL 2.9 33.4 + - - -
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Residues in contact with ARG 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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76A LYS* 4.4 5.9 - - - +
127A VAL 3.2 10.3 + - - +
128A THR* 3.7 10.1 - - - +
130A GLU* 1.3 81.1 - - - +
132A ASP* 1.3 68.7 + - - +
134A MET 3.5 0.2 + - - -
135A SER* 2.8 35.0 + - - +
145A LEU* 3.8 21.9 - - + +
148A THR* 3.0 24.8 + - + +
150A GLN* 5.6 0.2 - - - +
157A PHE* 4.2 17.7 - - + -
1368A SO4 2.8 41.4 + - - -
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Residues in contact with ASP 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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128A THR* 3.0 38.1 + - - +
129A ARG* 3.9 6.1 + - - +
131A ARG* 1.3 85.6 + - - +
133A VAL* 1.3 64.6 + - + +
135A SER* 3.4 8.1 + - - -
136A ARG* 3.2 28.2 + - - +
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Residues in contact with VAL 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 ARG* 2.8 41.1 + - + +
130A GLU 4.1 1.8 - - - +
132A ASP* 1.3 72.2 - - + +
134A MET* 1.3 64.7 + - - +
136A ARG* 2.9 22.3 + - - +
137A LEU* 3.3 16.7 + - + +
201A ILE* 4.0 23.6 - - + -
224A PHE* 3.8 37.2 - - + +
227A ALA* 4.6 5.6 - - + -
229A VAL* 3.9 22.2 - - + -
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Residues in contact with MET 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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130A GLU* 3.0 41.1 + - - +
133A VAL* 1.3 74.6 - - - +
135A SER* 1.3 61.1 + - - +
137A LEU* 3.2 28.1 + - - +
143A VAL* 3.2 53.5 - - + +
144A LYS* 4.7 2.0 - - - -
145A LEU* 3.9 27.0 + - + +
157A PHE* 6.0 0.7 - - - -
159A LEU* 3.9 22.4 - - + -
222A THR* 4.1 11.4 - - - +
224A PHE* 4.0 26.5 - - + -
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Residues in contact with SER 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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131A ARG* 2.8 29.8 + - - +
132A ASP* 3.6 8.2 - - - -
133A VAL 3.2 0.4 - - - -
134A MET* 1.3 75.6 - - - +
136A ARG* 1.3 61.0 + - - +
137A LEU 4.4 3.2 - - - +
145A LEU* 4.0 18.4 - - - +
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Residues in contact with ARG 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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132A ASP* 3.2 21.1 - - - +
133A VAL* 2.9 11.3 + - - +
135A SER* 1.3 79.1 - - - +
137A LEU* 1.3 66.5 + - + +
138A ASP* 3.7 3.0 + - - +
195A TYR* 3.8 0.2 + - - -
199A LYS* 3.3 57.0 + - + +
201A ILE* 4.1 13.8 - - + +
229A VAL* 3.6 32.5 - - - +
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Residues in contact with LEU 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 VAL* 3.4 18.6 - - + +
134A MET* 3.2 18.4 + - + +
135A SER 4.4 3.3 - - - +
136A ARG* 1.3 81.1 - - - +
138A ASP* 1.3 60.4 + - - +
139A HIS 3.9 0.7 - - - -
142A PHE* 3.8 24.0 - - + -
143A VAL 5.3 3.6 - - - +
144A LYS* 5.5 7.8 - - - +
195A TYR* 3.8 21.1 - - + -
196A LEU* 3.8 21.3 - - + -
199A LYS* 4.5 3.6 - - + -
201A ILE* 4.2 13.7 - - + -
224A PHE* 3.6 42.8 - - + -
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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