Contacts of the helix formed by residues 127 - 138 (chain A) in PDB entry 2FHP
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A TYR* 4.2 2.4 + - - -
100A ALA* 5.7 0.9 - - - +
101A ASN* 3.0 34.9 + - - +
121A PRO* 4.8 1.6 - - - +
125A LYS* 3.4 18.4 + - - +
126A GLN* 1.3 78.9 - - - +
128A ILE* 1.3 65.4 + - - +
129A VAL 3.3 2.8 + - - -
130A SER* 3.3 18.0 + - - +
131A GLN* 2.9 40.2 + - - +
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Residues in contact with ILE 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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119A LEU* 4.1 16.8 - - + +
121A PRO* 4.2 18.6 - - + -
126A GLN* 2.9 24.9 + - + +
127A GLU* 1.3 76.7 - - - +
129A VAL* 1.3 59.3 + - - +
131A GLN* 3.3 8.8 + - - +
132A LEU* 2.9 43.7 + - + +
149A CYS* 3.8 33.9 - - + -
151A THR* 3.5 32.5 - - + -
157A LEU* 4.3 16.2 - - + -
161A ILE* 4.9 3.6 - - + -
180A TYR* 5.1 0.7 - - + -
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Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLN* 4.4 1.5 + - - +
127A GLU 3.3 0.8 - - - -
128A ILE* 1.3 76.3 - - - +
130A SER* 1.3 57.9 + - - +
132A LEU* 3.3 1.6 + - - +
133A GLU* 2.9 49.5 + - - +
157A LEU* 4.6 9.6 - - + -
158A PRO* 3.6 36.6 - - + -
161A ILE* 4.0 23.5 - - + +
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Residues in contact with SER 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 ASN* 5.8 0.2 + - - -
127A GLU* 3.3 22.7 + - - -
129A VAL* 1.3 78.4 - - - +
131A GLN* 1.3 57.4 + - - +
133A GLU* 3.3 15.7 + - - +
134A LYS* 2.9 28.1 + - - +
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Residues in contact with GLN 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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48A LEU* 3.7 25.1 - - + +
49A TYR* 3.0 31.3 + - - -
100A ALA* 3.9 6.9 - - - +
101A ASN* 3.1 29.3 + - - +
104A LEU* 3.9 15.4 - - + +
119A LEU* 4.5 9.7 - - + +
121A PRO* 5.7 0.3 - - - +
127A GLU* 2.9 37.0 + - + +
128A ILE* 3.7 9.6 - - - +
130A SER* 1.3 78.3 - - - +
132A LEU* 1.3 59.0 + - + +
134A LYS* 3.1 5.7 + - - +
135A MSE 2.9 34.7 + - + +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.9 12.3 - - + -
128A ILE* 2.9 29.9 + - + +
129A VAL 3.9 3.1 - - - +
131A GLN* 1.3 72.3 - - - +
133A GLU* 1.3 61.7 + - - +
135A MSE 3.2 20.0 + - + +
136A LEU* 2.9 33.5 + - - +
141A LEU* 5.4 0.4 - - + -
147A ILE* 3.8 44.2 - - + -
161A ILE* 3.7 34.5 - - + -
164A LEU* 4.0 15.4 - - + +
180A TYR* 4.2 9.0 - - + -
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Residues in contact with GLU 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 VAL* 2.9 37.1 + - - +
130A SER* 3.6 14.2 + - - +
132A LEU* 1.3 77.2 - - - +
134A LYS* 1.3 55.2 + - - +
136A LEU* 3.3 8.5 + - + +
137A GLU* 2.9 29.3 + - - +
161A ILE* 3.8 15.9 - - + +
162A GLY* 5.4 4.0 - - - +
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Residues in contact with LYS 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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101A ASN 5.6 0.4 - - - +
104A LEU* 4.1 26.0 - - + -
105A GLU* 2.9 31.1 + - + +
130A SER 2.9 14.2 + - - +
131A GLN* 3.4 12.6 - - - +
133A GLU* 1.3 73.5 - - - +
135A MSE 1.3 59.3 + - - +
137A GLU* 2.9 30.1 + - - +
138A ARG* 2.9 53.5 + - + +
140A LEU* 5.5 0.2 - - + -
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Residues in contact with MSE 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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46A LEU* 3.9 10.1 - - + -
48A LEU* 6.0 0.7 - - - -
104A LEU* 4.1 22.9 - - + -
114A PHE* 3.8 17.7 - - + -
117A VAL* 3.7 42.6 - - + -
119A LEU* 5.5 2.5 - - - -
131A GLN* 2.9 19.6 + - - +
132A LEU* 3.2 20.6 + - + +
134A LYS* 1.3 74.8 - - - +
136A LEU* 1.3 58.2 + - - +
139A GLN* 3.1 6.8 + - - -
140A LEU* 2.9 61.1 + - + -
141A LEU* 3.8 19.3 + - + +
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Residues in contact with LEU 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 LEU 2.9 18.3 + - - +
133A GLU* 3.7 10.1 - - + +
135A MSE 1.3 74.8 - - - +
137A GLU* 1.3 66.2 + - - +
139A GLN* 3.2 18.0 + - - +
141A LEU* 3.9 22.4 - - + -
161A ILE* 3.5 29.6 - - + +
162A GLY* 4.0 6.7 - - - -
163A THR* 3.5 30.5 - - + +
164A LEU* 4.1 14.8 - - + -
182A GLN* 4.2 9.9 - - - +
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Residues in contact with GLU 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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108A TYR* 5.6 0.7 - - - -
133A GLU 2.9 17.0 + - - +
134A LYS* 2.9 38.1 + - - +
136A LEU* 1.3 79.1 - - - +
138A ARG* 1.3 85.2 + - - +
139A GLN* 3.6 6.1 + - - +
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Residues in contact with ARG 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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104A LEU 5.1 0.9 - - - +
105A GLU* 2.8 39.2 + - - +
108A TYR* 3.5 59.8 + - + -
134A LYS* 2.9 36.9 + - + +
137A GLU* 1.3 103.6 + - - +
139A GLN* 1.3 70.7 + - - +
140A LEU* 3.3 21.4 + - + +
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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