Contacts of the helix formed by residues 126 - 138 (chain B) in PDB entry 1F3F
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 SER 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B VAL* 3.5 13.2 - - - +
124B SER* 4.1 0.2 - - - -
125B ASP* 1.3 82.3 + - - +
127B VAL* 1.3 59.7 + - - +
128B GLU* 3.3 24.9 + - - +
129B SER* 3.0 27.4 + - - -
130B ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 127 (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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9B GLU* 3.5 40.2 - - + +
10B ARG 5.4 1.3 - - - +
88B VAL* 4.1 10.0 - - + +
126B SER* 1.3 72.6 - - - +
128B GLU* 1.3 72.7 + - + +
130B ALA* 3.4 1.9 + - - +
131B ASN* 3.0 41.4 + - - +
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Residues in contact with GLU 128 (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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126B SER* 3.3 17.7 + - - +
127B VAL* 1.3 92.4 + - + +
129B SER* 1.3 62.5 + - - +
131B ASN* 3.3 9.7 + - - +
132B ARG* 3.1 21.8 + - - +
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 5.2 5.4 + - - -
125B ASP* 3.2 22.9 + - - -
126B SER* 3.0 22.6 + - - -
128B GLU* 1.3 75.6 - - - +
130B ALA* 1.3 53.4 + - - +
132B ARG* 3.3 10.9 + - - +
133B GLU* 2.7 56.5 + - - +
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Residues in contact with ALA 130 (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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10B ARG 3.4 25.1 - - - +
11B THR* 3.9 5.8 - - - -
12B PHE 4.7 0.2 - - - +
88B VAL* 4.0 4.5 - - + -
124B SER* 3.3 25.7 - - - +
126B SER 2.9 17.1 + - - +
127B VAL 3.5 4.7 - - - +
129B SER* 1.3 74.8 - - - +
131B ASN* 1.3 57.4 + - - +
133B GLU* 3.9 0.6 - - - +
134B ILE* 2.7 41.9 + - - +
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Residues in contact with ASN 131 (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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10B ARG* 4.9 6.6 + - - +
127B VAL* 3.0 36.2 + - - +
128B GLU* 3.8 6.4 - - - +
130B ALA* 1.3 76.7 - - - +
132B ARG* 1.3 62.6 + - - +
134B ILE* 3.9 13.0 - - - +
135B ALA* 3.2 23.6 + - - +
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Residues in contact with ARG 132 (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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54B SER* 2.2 45.1 + - - +
55B HIS* 3.6 15.0 + - - +
57B ALA* 3.4 18.3 - - - +
58B GLU* 5.5 3.0 + - - +
128B GLU 3.1 13.4 + - - +
129B SER* 3.4 13.8 - - - +
131B ASN* 1.3 78.4 - - - +
133B GLU* 1.3 75.8 + - - +
135B ALA* 3.2 8.6 + - - +
136B LEU* 3.1 31.3 + - + +
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Residues in contact with GLU 133 (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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12B PHE* 3.7 24.0 - - + -
55B HIS* 3.7 32.9 + - - +
58B GLU* 5.0 5.9 - - - +
123B GLY 4.5 1.1 - - - +
124B SER* 2.7 35.6 + - - -
125B ASP* 5.2 0.7 + - - -
129B SER* 2.7 35.0 + - - +
130B ALA 3.9 2.7 - - - +
132B ARG* 1.3 88.2 + - - +
134B ILE* 1.3 62.8 + - - +
136B LEU* 3.0 18.3 + - + -
137B TRP* 3.0 20.6 + - - -
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Residues in contact with ILE 134 (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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10B ARG* 3.7 30.5 - - + +
11B THR 4.2 1.3 - - - +
12B PHE* 3.9 19.3 - - + -
81B VAL* 3.6 35.9 - - + -
130B ALA 2.7 34.7 + - - +
131B ASN* 3.9 11.0 - - - +
133B GLU* 1.3 72.0 - - - +
135B ALA* 1.3 58.2 + - - +
138B PHE* 2.9 31.4 + - + +
143B LEU* 3.6 29.4 - - + -
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Residues in contact with ALA 135 (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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131B ASN 3.2 14.6 + - - +
132B ARG* 3.5 10.5 - - - +
134B ILE* 1.3 77.6 - - - +
136B LEU* 1.3 62.8 + - - +
138B PHE 3.6 14.0 - - - +
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Residues in contact with LEU 136 (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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51B LEU* 3.7 17.7 - - + +
54B SER* 3.4 39.3 - - - +
55B HIS* 3.5 28.7 - - + +
132B ARG* 3.1 29.2 + - + +
133B GLU* 3.0 14.0 + - - +
135B ALA* 1.3 79.3 - - - +
137B TRP* 1.3 66.7 + - + +
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Residues in contact with TRP 137 (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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12B PHE* 3.3 35.5 - + + -
14B ALA* 4.9 3.1 - - + -
43B LYS* 2.7 37.2 + - - -
45B LEU* 3.9 22.7 - - + -
47B PRO* 3.9 24.5 - - + -
51B LEU* 3.6 38.0 - - + +
55B HIS* 3.1 44.2 + + + +
72B ILE* 4.9 9.0 - - + -
77B VAL* 4.1 15.7 - - + -
79B ALA* 3.7 16.4 - - + -
133B GLU 3.0 26.5 + - - +
136B LEU* 1.3 88.2 - - + +
138B PHE* 1.3 59.2 + - + +
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Residues in contact with PHE 138 (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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12B PHE* 3.9 20.4 - + - -
41B GLY* 3.7 5.8 - - - -
42B LEU 3.4 25.6 - - - -
43B LYS* 4.0 18.6 - - + -
79B ALA* 3.5 32.1 - - + -
80B MET* 4.0 1.3 - - - -
81B VAL* 3.4 24.0 - - + -
134B ILE 2.9 19.9 + - - +
135B ALA* 3.6 14.9 - - - +
136B LEU 3.7 0.4 - - - -
137B TRP* 1.3 85.9 - - + +
139B LYS* 1.3 68.0 + - - +
140B PRO* 3.9 2.6 - - - +
142B GLU* 3.2 26.0 - - + -
143B LEU* 3.8 23.4 - - + +
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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