Contacts of the helix formed by residues 141 - 157 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B LYS* 3.1 33.6 + - - +
106B THR* 4.6 2.3 + - - -
135B ALA* 4.0 0.4 - - - -
140B MET* 1.3 74.2 - - - +
142B LYS* 1.3 65.5 + - - +
143B GLU* 4.2 8.0 - - + +
144B VAL* 3.3 18.4 + - + +
145B ILE* 3.1 24.8 + - - +
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B SER* 2.9 43.8 + - - +
131B ILE* 3.4 28.7 - - + +
132B THR* 3.0 23.1 + - + +
135B ALA* 3.8 14.6 - - + +
140B MET 3.8 2.2 + - - -
141B GLU* 1.3 70.7 - - - +
143B GLU* 1.3 67.3 + - - +
145B ILE 3.3 1.2 + - - -
146B ARG* 3.0 31.9 + - + +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS* 5.9 0.9 - - - +
141B GLU* 3.1 10.0 - - + +
142B LYS* 1.3 80.3 - - - +
144B VAL* 1.3 60.6 + - + +
145B ILE 3.0 1.3 - - - -
146B ARG* 2.6 70.1 + - - +
147B VAL* 2.9 20.1 + - + +
19N T 5.8 3.8 - - - +
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS* 3.0 33.2 - - - +
106B THR* 3.5 20.0 - - + +
108B ILE* 4.9 8.1 - - + -
140B MET* 3.8 27.6 - - + -
141B GLU* 3.3 26.4 + - + +
143B GLU* 1.3 78.3 - - - +
145B ILE* 1.3 57.8 + - + +
147B VAL* 3.6 3.6 + - - +
148B TRP* 3.0 26.8 + - + +
17N A 5.4 1.1 - - - -
18N A 3.8 20.3 + - - +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.9 25.1 - - + -
131B ILE* 3.8 18.6 - - + -
134B ILE* 4.3 15.7 - - + -
135B ALA* 4.0 12.8 - - + -
138B LEU* 4.5 4.7 - - + -
140B MET* 3.7 39.0 - - + -
141B GLU 3.1 14.6 + - - +
142B LYS 3.6 7.2 - - - +
143B GLU 3.0 0.6 - - - -
144B VAL* 1.3 77.4 - - + +
146B ARG* 1.3 64.5 + - - +
148B TRP* 3.4 3.6 + - + +
149B PHE* 3.2 43.4 + - + -
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 3.9 27.3 - - + +
142B LYS* 3.0 23.4 + - + +
143B GLU* 2.6 48.5 + - - +
145B ILE* 1.3 72.9 - - - +
147B VAL* 1.3 75.5 + - - +
149B PHE* 3.3 6.4 + - - +
150B SER* 3.2 28.3 + - - -
153B ARG* 4.4 5.2 + - - +
1M C 4.6 21.1 - - - -
19N T 5.4 4.2 - - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLU* 2.9 23.0 + - + +
144B VAL 3.8 6.5 - - - +
146B ARG* 1.3 95.0 - - - +
148B TRP* 1.3 59.1 + - - +
150B SER* 2.7 28.0 + - - +
151B ASN* 2.8 37.8 + - - +
17N A 4.4 2.5 - - + -
18N A 3.9 32.5 - - + +
19N T 4.0 18.2 - - + +
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Residues in contact with TRP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE* 3.5 26.2 - - + +
113B ARG* 3.4 34.6 - - + +
116B LEU* 3.6 55.3 - - + +
117B GLU* 3.8 9.2 - - - -
120B PHE* 4.1 7.9 - - + -
144B VAL* 3.0 16.1 + - + +
145B ILE* 3.6 10.3 - - + +
147B VAL* 1.3 79.9 - - - +
149B PHE* 1.3 81.5 + + + +
151B ASN* 3.6 2.5 + - - +
152B ARG* 2.9 54.8 + - + +
17N A 3.4 31.3 + - - -
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 4.2 19.5 - - + -
119B SER* 3.8 19.7 - - - -
120B PHE* 3.9 31.1 - + + -
123B ASN 4.0 3.1 - - - -
124B GLN 3.6 8.5 - - - -
126B PRO* 3.4 40.4 - - + -
131B ILE* 5.2 3.6 - - + -
134B ILE* 4.3 7.4 - - + -
145B ILE* 3.2 38.5 + - + +
146B ARG* 3.3 9.2 + - - +
147B VAL 3.1 0.8 - - - -
148B TRP* 1.3 91.6 - + - +
150B SER* 1.3 64.8 + - - +
152B ARG* 3.8 3.1 - - - +
153B ARG* 3.0 41.6 + - - +
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG* 3.2 18.0 + - - -
147B VAL* 2.7 18.1 + - - -
149B PHE* 1.3 70.1 - - - +
151B ASN* 1.3 63.0 + - - -
153B ARG* 3.0 25.2 + - - +
154B GLN* 2.8 33.2 + - - +
1M C 5.7 0.5 - - - -
2M A 3.9 14.7 + - - -
3M C 4.3 19.2 + - - -
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Residues in contact with ASN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 2.8 28.1 + - - +
148B TRP* 3.9 4.0 - - - +
150B SER* 1.3 77.3 - - - +
152B ARG* 1.3 58.3 + - - +
154B GLN* 2.8 20.8 + - - +
155B LYS* 2.7 30.9 + - - +
3M C 5.8 0.2 + - - -
16N A 5.3 4.9 - - + -
17N A 3.2 45.8 + - - +
18N A 3.2 30.5 + - - +
19N T 4.5 3.3 - - - +
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ARG* 4.9 5.3 - - - +
117B GLU* 2.8 40.0 + - - -
120B PHE* 3.6 32.8 - - + -
121B LEU* 5.8 1.8 - - - +
148B TRP* 2.9 45.1 + - + +
149B PHE 3.9 4.7 - - - +
150B SER 3.2 0.2 - - - -
151B ASN* 1.3 76.8 - - - +
153B ARG* 1.3 61.6 + - - +
155B LYS* 3.7 31.0 + - - +
156B GLU* 2.7 36.5 + - - +
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PHE* 4.1 11.4 - - + -
124B GLN* 2.8 41.8 + - + +
125B LYS* 3.9 23.9 - - - +
126B PRO* 4.4 0.8 - - - +
146B ARG* 4.4 5.5 + - - +
149B PHE* 3.0 42.4 + - - +
150B SER* 3.0 32.6 + - - +
151B ASN 3.0 0.8 - - - -
152B ARG* 1.3 76.5 - - - +
154B GLN* 1.3 64.6 + - + +
156B GLU* 3.0 20.9 + - - +
157B LYS* 3.2 8.5 + - - +
1M C 4.4 13.0 + - - -
2M A 2.8 43.4 + - - +
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Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B SER* 2.8 17.9 + - - +
151B ASN* 2.8 22.3 + - - +
153B ARG* 1.3 72.7 - - + +
155B LYS* 1.3 60.5 + - - +
156B GLU 3.0 1.8 - - - -
157B LYS* 2.8 27.5 + - - +
158B ARG* 3.3 23.0 + - - +
2M A 5.9 1.1 - - + -
3M C 3.1 44.9 - - + +
4M A 3.1 41.2 + - - +
5M T 4.6 3.3 + - - +
18N A 4.4 2.8 - - - +
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Residues in contact with LYS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ARG* 5.1 9.9 - - - +
151B ASN 2.7 18.4 + - - +
152B ARG* 3.8 32.6 - - - +
154B GLN* 1.3 74.1 - - - +
156B GLU* 1.3 61.7 + - - +
158B ARG* 3.4 46.7 + - - +
159B ILE* 4.9 0.9 - - - +
16N A 2.8 40.6 + - - +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PHE* 4.1 12.3 - - + -
152B ARG* 2.7 40.1 + - - +
153B ARG* 3.0 16.1 + - - +
154B GLN 3.0 0.4 - - - -
155B LYS* 1.3 81.7 - - - +
157B LYS* 1.3 54.9 + - - +
158B ARG 3.1 5.4 + - - -
159B ILE* 4.0 26.4 - - - +
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ARG 3.2 10.0 + - - +
154B GLN* 2.8 15.0 + - - +
156B GLU* 1.3 76.3 - - - +
158B ARG* 1.3 59.9 + - + +
159B ILE* 4.0 2.3 + - - -
3M C 2.8 43.1 + - + +
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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