Contacts of the helix formed by residues 141 - 157 (chain A) in PDB entry 1HF0
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 GLU 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS* 4.1 21.6 + - - -
106A THR* 5.2 3.1 + - - +
135A ALA* 4.2 0.7 - - - -
140A MET* 1.3 73.5 - - - +
142A LYS* 1.3 69.0 + - - +
143A GLU* 4.4 6.2 - - + +
144A VAL* 2.9 36.2 + - + +
145A ILE* 3.1 9.0 + - - +
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Residues in contact with LYS 142 (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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128A SER* 2.6 40.4 + - - +
131A ILE* 3.6 19.9 - - + +
132A THR* 2.7 37.0 - - + +
135A ALA* 3.8 13.3 - - + +
140A MET 3.5 3.6 + - - -
141A GLU* 1.3 71.6 - - - +
143A GLU* 1.3 57.1 + - - +
145A ILE* 3.1 4.7 + - - +
146A ARG* 2.9 33.4 + - + +
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Residues in contact with GLU 143 (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 LYS* 6.3 3.4 - - + -
141A GLU* 3.1 6.8 - - + +
142A LYS* 1.3 78.2 - - - +
144A VAL* 1.3 63.8 + - + +
146A ARG* 2.9 45.1 + - - +
147A VAL* 3.0 32.6 + - + +
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Residues in contact with VAL 144 (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 LYS* 4.2 14.8 - - - -
106A THR* 3.7 18.8 - - + +
108A ILE* 4.2 24.7 - - + -
140A MET* 4.5 9.9 - - + -
141A GLU* 2.9 32.4 + - + +
143A GLU* 1.3 74.2 - - + +
145A ILE* 1.3 68.0 + - + +
147A VAL* 3.1 4.9 + - - +
148A TRP* 2.8 29.3 + - + +
16M A 5.9 0.2 - - - -
17M A 3.7 25.7 + - - +
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Residues in contact with ILE 145 (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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116A LEU* 3.9 28.9 - - + -
131A ILE* 3.5 28.3 - - + +
134A ILE* 4.1 15.3 - - + -
135A ALA* 3.8 15.9 - - + +
138A LEU* 4.3 4.5 - - + -
140A MET* 3.7 31.9 - - + -
141A GLU 3.1 9.6 + - - +
142A LYS 3.1 9.0 + - - +
144A VAL* 1.3 83.0 - - + +
146A ARG* 1.3 61.5 + - - +
148A TRP* 3.2 5.2 + - + +
149A PHE* 3.1 36.0 + - + -
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Residues in contact with ARG 146 (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 ILE* 3.8 29.4 - - + -
142A LYS* 2.9 18.7 + - - +
143A GLU* 2.9 43.2 + - - +
145A ILE* 1.3 77.9 - - - +
147A VAL* 1.3 74.0 + - - +
149A PHE* 3.5 4.2 + - - +
150A SER* 3.3 26.2 + - - -
153A ARG* 5.3 0.7 + - - -
18M T 5.2 5.5 - - - +
1N C 4.2 20.3 - - - -
2N T 2.7 58.3 + - - +
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Residues in contact with VAL 147 (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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143A GLU* 3.0 33.3 + - + +
144A VAL* 3.6 7.9 - - - +
146A ARG* 1.3 85.5 - - - +
148A TRP* 1.3 68.1 + - - +
150A SER* 3.0 8.9 + - - -
151A ASN* 2.8 44.4 + - - +
16M A 4.8 5.2 - - + -
17M A 3.8 26.7 - - + +
18M T 3.8 17.0 - - + -
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Residues in contact with TRP 148 (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 ILE* 4.4 19.8 - - + +
113A ARG* 4.8 14.6 - - + +
116A LEU* 3.4 67.4 - - + +
117A GLU* 4.0 7.0 - - - -
120A PHE* 4.1 2.7 - - + -
144A VAL* 2.8 19.3 + - + +
145A ILE* 3.2 9.6 + - + +
147A VAL* 1.3 78.7 - - - +
149A PHE* 1.3 89.3 + + - +
151A ASN* 3.4 3.7 + - - +
152A ARG* 2.8 59.7 + - + +
16M A 3.2 33.6 + - - -
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Residues in contact with PHE 149 (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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116A LEU* 3.9 16.6 - - + -
119A SER* 3.4 27.1 - - - -
120A PHE* 3.8 22.2 - + + -
123A ASN 3.6 20.2 - - - -
124A GLN 3.8 9.0 - - - -
126A PRO* 3.4 34.8 - - + -
131A ILE* 5.2 4.0 - - + -
134A ILE* 4.2 10.3 - - + -
145A ILE* 3.1 29.5 + - + +
146A ARG* 3.8 8.5 - - - +
147A VAL 3.1 0.2 - - - -
148A TRP* 1.3 98.6 - + - +
150A SER* 1.3 58.6 - - - +
152A ARG* 3.1 3.1 + - - +
153A ARG* 2.8 44.4 + - - +
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Residues in contact with SER 150 (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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146A ARG* 3.3 19.0 + - - -
147A VAL* 3.0 13.1 + - - -
149A PHE* 1.3 77.3 - - - +
151A ASN* 1.3 61.9 + - - +
153A ARG* 3.2 26.7 + - - +
154A GLN* 2.9 34.0 + - - +
2N T 5.0 2.0 + - - -
3N C 4.1 13.0 + - - -
4N C 4.2 18.6 + - - -
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Residues in contact with ASN 151 (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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147A VAL* 2.8 28.9 + - - +
148A TRP* 3.8 5.6 - - - +
150A SER* 1.3 76.1 - - - +
152A ARG* 1.3 58.3 + - - +
154A GLN* 3.0 16.9 + - - +
155A LYS* 2.7 29.2 + - - +
158A ARG* 5.1 0.5 + - - -
15M A 5.3 4.9 - - + -
16M A 3.2 36.5 + - - +
17M A 3.2 43.3 + - - +
18M T 4.5 1.9 - - - +
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Residues in contact with ARG 152 (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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117A GLU* 2.4 35.5 + - - -
120A PHE* 3.5 29.5 - - + -
121A LEU* 5.7 1.4 - - - +
148A TRP* 2.8 49.0 + - + +
149A PHE* 3.1 5.8 + - - +
151A ASN* 1.3 77.8 - - - +
153A ARG* 1.3 61.3 + - - +
155A LYS* 3.2 29.4 + - - +
156A GLU* 2.5 44.2 + - - +
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Residues in contact with ARG 153 (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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120A PHE* 4.1 10.1 - - + -
124A GLN* 3.1 33.8 + - + +
125A LYS* 3.8 25.4 - - - +
126A PRO* 4.7 1.2 + - - +
146A ARG 5.3 0.6 + - - -
149A PHE* 2.8 34.6 + - - +
150A SER* 3.2 23.3 + - - +
152A ARG* 1.3 72.3 - - - +
154A GLN* 1.3 64.8 + - + +
156A GLU* 2.9 10.6 + - - +
157A LYS* 2.9 30.9 + - + +
2N T 3.3 30.4 + - - -
3N C 2.6 45.5 + - - +
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Residues in contact with GLN 154 (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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150A SER* 2.9 20.9 + - - +
151A ASN* 3.3 22.6 + - - +
153A ARG* 1.3 76.9 - - + +
155A LYS* 1.3 63.2 + - - +
157A LYS* 3.0 18.7 + - - +
158A ARG* 3.4 28.1 + - - +
17M A 4.3 1.8 - - - +
3N C 6.0 0.4 - - + -
4N C 3.1 36.8 - - + +
5N A 2.9 50.2 + - - +
6N T 4.4 2.8 + - - +
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Residues in contact with LYS 155 (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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117A GLU* 5.9 0.4 + - - -
151A ASN 2.7 16.4 + - - +
152A ARG* 3.3 36.3 - - - +
154A GLN* 1.3 70.7 - - - +
156A GLU* 1.3 67.2 + - - +
158A ARG* 2.9 47.3 + - - +
159A ILE* 5.4 0.2 - - - +
14M C 5.2 0.4 - - - -
15M A 2.9 40.9 + - + +
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Residues in contact with GLU 156 (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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120A PHE* 4.3 14.4 - - + -
124A GLN* 5.9 1.6 - - + -
152A ARG* 2.5 53.4 + - - +
153A ARG* 3.2 15.0 - - - +
155A LYS* 1.3 78.0 - - - +
157A LYS* 1.3 57.3 + - - +
158A ARG 3.2 7.4 + - - +
159A ILE* 4.1 19.0 - - - +
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Residues in contact with LYS 157 (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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153A ARG* 2.9 19.0 + - + +
154A GLN* 3.4 13.9 - - - +
155A LYS 3.0 1.0 + - - -
156A GLU* 1.3 75.2 - - + +
158A ARG* 1.3 58.6 + - + +
159A ILE 4.1 0.5 + - - -
3N C 4.0 16.6 + - - -
4N C 2.5 39.0 + - - +
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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
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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