Contacts of the helix formed by residues 127 - 142 (chain A) in PDB entry 1HFC
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 ARG 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A TYR* 3.7 61.0 + - + -
125A LEU 3.6 2.0 + - - +
126A PRO* 1.3 70.0 - - - +
128A ALA* 1.3 58.6 + - - +
130A VAL* 3.0 5.3 + - - +
131A ASP* 2.9 34.7 + - - +
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Residues in contact with ALA 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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126A PRO* 3.2 5.0 - - + +
127A ARG* 1.3 77.2 - - - +
129A ASP* 1.3 62.0 + - - +
131A ASP* 3.4 9.1 + - - +
132A HIS* 2.9 30.8 + - - +
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Residues in contact with ASP 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 LEU* 4.3 15.1 - - + +
126A PRO* 2.9 37.7 + - + +
128A ALA* 1.3 77.5 - - - +
130A VAL* 1.3 61.8 - - - +
132A HIS* 3.8 6.5 - - - +
133A ALA* 2.9 30.5 + - - +
205A ASN* 3.3 29.3 + - + +
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Residues in contact with VAL 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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118A ILE* 4.7 5.2 - - + -
121A TYR* 3.6 27.6 - - + -
122A THR* 3.9 30.3 - - + +
125A LEU* 4.0 11.4 - - + +
126A PRO 3.3 10.3 + - - +
127A ARG 3.0 7.4 + - - +
129A ASP* 1.3 75.1 - - - +
131A ASP* 1.3 67.5 + - - +
132A HIS 3.3 0.2 + - - -
133A ALA* 3.3 1.9 + - - +
134A ILE* 3.1 30.7 + - + +
163A PHE* 4.0 20.9 - - + -
212A LEU* 4.1 17.9 - - + -
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Residues in contact with ASP 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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116A TYR* 5.1 0.9 + - - -
118A ILE* 3.4 16.9 - - - +
121A TYR* 2.5 32.6 + - - -
127A ARG* 2.9 20.5 + - - +
128A ALA* 3.6 11.6 - - - +
130A VAL* 1.3 77.1 - - - +
132A HIS* 1.3 57.3 + - - +
134A ILE* 3.3 1.4 + - - +
135A GLU* 2.8 36.5 + - - +
151A LYS* 3.8 19.9 + - - +
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Residues in contact with HIS 132 (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 ALA 2.9 18.2 + - - +
129A ASP* 3.8 8.3 - - - +
130A VAL 3.2 0.2 - - - -
131A ASP* 1.3 72.4 - - - +
133A ALA* 1.3 61.1 + - - +
135A GLU* 3.9 15.2 - - + +
136A LYS* 2.8 81.0 + - + +
139A GLN* 6.1 0.6 + - - -
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Residues in contact with ALA 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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125A LEU* 6.0 0.7 - - + -
129A ASP 2.9 18.8 + - - +
130A VAL 3.7 3.8 - - - +
132A HIS* 1.3 78.2 + - - +
134A ILE* 1.3 63.2 + - - +
136A LYS* 4.4 4.5 - - - +
137A ALA* 3.3 10.0 + - - +
212A LEU* 4.2 16.2 - - + -
213A HIS* 3.0 55.9 + - + +
216A ALA* 4.5 0.2 - - - +
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Residues in contact with ILE 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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116A TYR* 3.8 13.5 - - + -
118A ILE* 4.1 16.8 - - + -
130A VAL* 3.1 23.0 + - + +
131A ASP 3.8 2.7 - - - +
133A ALA* 1.3 74.1 - - - +
135A GLU* 1.3 69.6 - - - +
137A ALA* 3.1 5.2 + - - +
138A PHE* 3.1 45.5 + - + -
161A ILE* 3.8 24.0 - - + -
163A PHE* 5.8 1.6 - - + -
197A PHE* 4.5 12.6 - - + -
212A LEU* 4.8 12.3 - - + -
216A ALA* 3.5 27.6 - - + -
220A LEU* 4.9 2.9 - - + -
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Residues in contact with GLU 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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116A TYR* 3.8 21.2 + - - +
131A ASP* 2.8 21.7 + - - +
132A HIS* 3.9 15.1 - - + +
134A ILE* 1.3 79.0 - - - +
136A LYS* 1.4 57.2 + - - +
138A PHE* 3.2 7.3 + - - +
139A GLN* 3.0 48.3 + - - +
151A LYS* 6.0 1.6 - - - +
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Residues in contact with LYS 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 HIS* 2.8 66.3 + - + +
133A ALA* 4.4 2.6 - - - +
135A GLU* 1.4 70.3 - - - +
137A ALA* 1.3 64.0 + - - +
139A GLN* 3.3 21.7 + - + +
140A LEU* 3.2 27.8 + - + +
213A HIS* 3.5 34.7 + - + +
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Residues in contact with ALA 137 (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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133A ALA 3.3 15.6 + - - +
134A ILE 3.1 6.8 + - - +
136A LYS* 1.3 78.7 - - - +
138A PHE* 1.3 64.3 + - - +
140A LEU* 3.2 17.0 + - - +
141A TRP* 3.3 18.9 + - - -
213A HIS* 3.5 10.5 - - - +
216A ALA* 3.9 6.5 - - + -
217A ALA* 3.8 27.1 - - - +
220A LEU* 3.8 14.8 - - + -
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Residues in contact with PHE 138 (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 TYR* 3.4 52.3 - + + -
134A ILE* 3.1 35.1 + - + -
135A GLU* 3.6 7.0 - - - +
137A ALA* 1.3 75.8 - - - +
139A GLN* 1.3 60.0 - - - +
141A TRP* 3.1 9.5 + + - +
142A SER* 2.9 28.5 + - - -
149A PHE* 3.5 55.4 - + + -
159A ILE* 3.9 17.7 - - + -
161A ILE* 4.1 2.2 - - + -
220A LEU* 3.6 34.5 - - + +
224A LEU* 5.5 1.8 - - + -
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Residues in contact with GLN 139 (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 HIS* 6.1 0.4 + - - -
135A GLU* 3.0 36.9 + - - +
136A LYS* 3.6 30.4 - - + +
137A ALA 3.2 0.6 - - - -
138A PHE* 1.3 78.2 - - - +
140A LEU* 1.3 62.3 + - - +
142A SER* 3.2 11.6 + - - +
143A ASN* 2.9 39.9 + - - +
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Residues in contact with LEU 140 (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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136A LYS* 3.2 17.3 + - + +
137A ALA 3.5 7.0 - - - +
138A PHE 3.2 1.0 - - - -
139A GLN* 1.3 77.3 - - - +
141A TRP* 1.3 63.3 + - + +
143A ASN* 3.7 20.9 + - - +
144A VAL* 4.0 2.9 - - - +
213A HIS* 4.2 8.7 - - + +
217A ALA* 3.9 19.3 - - + -
235A LEU* 4.3 9.2 - - + -
246A VAL* 3.9 35.9 - - + +
247A GLN* 3.9 26.2 - - - +
248A LEU* 3.5 31.0 - - + +
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Residues in contact with TRP 141 (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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137A ALA 3.3 23.6 + - - -
138A PHE* 3.1 8.3 + + - +
140A LEU* 1.3 75.5 - - + +
142A SER* 1.3 67.0 - - - +
143A ASN 3.2 0.8 + - - -
144A VAL* 3.5 14.4 + - - +
145A THR* 2.9 20.1 + - - +
147A LEU* 5.6 0.9 - - + -
149A PHE* 4.8 4.0 - - + -
217A ALA* 3.1 32.9 + - + +
220A LEU* 4.1 13.6 - - + +
221A GLY* 3.7 17.0 - - - +
224A LEU* 3.9 23.8 - - + -
226A LEU* 3.5 28.5 - - + -
235A LEU* 5.0 3.8 - - + -
236A MET* 4.3 9.4 - - + -
248A LEU* 3.7 31.8 - - + +
252A ASP* 3.9 26.5 - - + -
256A ILE* 3.9 24.9 - - + -
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Residues in contact with SER 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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138A PHE 2.9 11.3 + - - -
139A GLN* 3.2 26.0 + - - +
141A TRP* 1.3 80.3 - - - +
143A ASN* 1.3 57.9 + - - +
145A THR* 2.9 25.8 - - - +
147A LEU 3.3 25.8 - - - +
148A THR* 4.9 1.3 - - - -
149A PHE* 4.0 16.4 - - - -
263A SER* 4.8 0.5 - - - -
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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