Contacts of the helix formed by residues 126 - 138 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A VAL* 3.6 12.1 - - - +
124A SER* 3.4 1.7 - - - -
125A ASP* 1.3 82.9 + - - +
127A VAL* 1.3 54.7 + - - +
128A GLU* 3.6 9.2 + - - +
129A SER* 3.1 25.8 + - - -
130A ALA* 2.7 34.8 + - - +
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Residues in contact with VAL 127 (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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9A GLU* 3.6 40.2 - - + +
10A ARG 5.8 1.1 - - - +
88A VAL* 4.1 5.3 - - + +
126A SER* 1.3 72.8 - - - +
128A GLU* 1.3 59.9 + - + +
130A ALA* 3.5 7.1 - - + +
131A ASN* 2.8 47.3 + - - +
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Residues in contact with GLU 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 SER* 3.2 8.2 + - - +
127A VAL* 1.3 81.1 - - + +
129A SER* 1.3 62.6 - - - +
131A ASN* 3.3 9.2 + - - +
132A ARG* 3.1 21.8 + - - +
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Residues in contact with SER 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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58A GLU* 5.2 4.7 + - - -
125A ASP* 2.8 32.4 + - - -
126A SER* 3.1 11.5 + - - -
128A GLU* 1.3 79.3 - - - +
130A ALA* 1.3 58.5 + - - +
132A ARG* 3.2 8.2 + - - +
133A GLU* 2.7 51.7 + - - +
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Residues in contact with ALA 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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10A ARG 3.4 25.4 - - - +
11A THR* 3.9 6.5 - - - -
12A PHE 4.7 0.2 - - - +
88A VAL* 4.0 5.4 - - + -
124A SER* 3.3 25.5 - - - +
126A SER 2.7 22.2 + - - +
127A VAL* 3.5 4.7 - - - +
129A SER* 1.3 72.9 - - - +
131A ASN* 1.3 59.4 + - - +
134A ILE* 2.8 37.4 + - + +
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Residues in contact with ASN 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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10A ARG* 5.3 2.4 - - - +
127A VAL* 2.8 40.4 + - - +
128A GLU* 3.7 7.1 - - - +
130A ALA* 1.3 73.6 - - - +
132A ARG* 1.3 62.6 + - - +
134A ILE* 3.6 11.9 + - - +
135A ALA* 3.2 23.9 + - - +
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Residues in contact with ARG 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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54A SER* 2.6 46.2 + - - +
55A HIS* 3.6 12.5 + - - +
57A ALA* 3.9 13.6 - - - +
58A GLU 5.8 0.6 - - - +
128A GLU 3.1 13.0 + - - +
129A SER* 3.6 9.9 - - - +
131A ASN* 1.3 75.8 - - - +
133A GLU* 1.3 68.8 + - + +
135A ALA* 3.4 7.5 + - - +
136A LEU* 3.0 35.1 + - + +
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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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12A PHE* 3.8 21.3 - - + -
55A HIS* 3.5 42.4 + - + +
58A GLU* 4.9 7.6 - - - +
123A GLY 4.3 1.4 - - - +
124A SER* 2.7 36.9 + - - +
125A ASP* 5.1 0.9 + - - -
129A SER* 2.7 36.5 + - - +
130A ALA 3.9 0.7 - - - +
132A ARG* 1.3 79.4 + - + +
134A ILE* 1.3 64.9 + - - +
136A LEU* 3.1 15.0 + - - -
137A TRP* 3.1 20.6 + - - -
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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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10A ARG* 3.8 39.7 - - + +
11A THR 4.2 1.8 - - - +
12A PHE* 4.1 15.0 - - + -
81A VAL* 3.7 27.8 - - + -
130A ALA 2.8 31.4 + - - +
131A ASN* 4.0 10.8 - - - +
133A GLU* 1.3 72.9 - - - +
135A ALA* 1.3 59.1 + - - +
138A PHE* 2.8 32.2 + - + +
143A LEU* 3.6 30.7 - - + -
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Residues in contact with ALA 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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131A ASN 3.2 16.5 + - - +
132A ARG* 3.6 6.3 - - - +
133A GLU 3.2 0.2 - - - -
134A ILE* 1.3 82.0 - - - +
136A LEU* 1.3 61.5 + - - +
138A PHE 3.6 14.6 + - - +
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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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51A LEU* 3.9 19.9 - - + +
54A SER* 3.6 24.7 - - - +
55A HIS* 3.5 43.5 - - + +
132A ARG* 3.0 31.9 + - + +
133A GLU* 3.1 10.1 + - - +
135A ALA* 1.3 78.3 - - - +
137A TRP* 1.3 66.9 + - + +
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Residues in contact with TRP 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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12A PHE* 3.3 37.1 - + + -
14A ALA* 5.1 2.9 - - + -
43A LYS* 2.6 35.9 + - - +
45A LEU* 3.8 24.9 - - + +
47A PRO* 3.8 26.7 - - + -
51A LEU* 3.7 36.4 - - + +
52A ALA* 5.7 1.3 - - - -
55A HIS* 3.0 43.9 + + + +
72A ILE* 5.1 8.3 - - + -
77A VAL* 4.1 18.4 - - + -
79A ALA* 3.8 15.3 - - + -
133A GLU 3.1 23.0 + - - +
136A LEU* 1.3 89.4 - - + +
138A PHE* 1.3 57.7 + - + +
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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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12A PHE* 3.9 18.2 - + - -
41A GLY* 3.7 5.4 - - - -
42A LEU 3.5 25.8 - - - -
43A LYS* 3.5 31.0 - - + -
79A ALA* 3.5 25.4 - - + -
80A MET 4.0 3.8 - - - -
81A VAL* 3.5 28.3 - - + -
134A ILE* 2.8 24.2 + - + +
135A ALA* 3.6 14.0 - - - +
136A LEU 3.6 0.6 - - - -
137A TRP* 1.3 82.7 - - + +
139A LYS* 1.3 63.4 + - - +
140A PRO* 3.9 2.1 - - - +
142A GLU* 3.6 15.0 - - + -
143A LEU* 3.7 29.9 - - + +
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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