Contacts of the helix formed by residues 131 - 139 (chain B) in PDB entry 1EFP
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 THR 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A AMP 2.8 56.9 + - - +
98B PRO* 3.2 30.7 - - - +
101B VAL* 3.8 23.3 - - + -
102B ALA* 4.2 3.2 - - - +
105B LEU* 3.9 14.8 - - + -
119B ALA* 5.7 1.3 - - + -
130B ALA* 1.3 71.3 - - - +
132B GLY* 1.3 59.1 + - - +
134B MET* 3.1 6.6 + - - +
135B LEU* 2.8 28.5 + - + +
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Residues in contact with GLY 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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400A AMP 4.7 4.8 + - - -
119B ALA* 4.7 6.7 - - - +
130B ALA 3.5 0.8 - - - -
131B THR* 1.3 77.7 - - - +
133B GLN* 1.3 58.1 + - - +
135B LEU* 3.1 7.7 + - - +
136B ALA* 2.9 26.2 + - - +
143B GLN* 5.9 1.1 - - - -
145B THR* 6.0 0.2 - - - -
177B VAL* 3.5 19.3 - - - +
179B THR* 3.9 25.1 - - - +
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LYS 2.7 28.0 + - - +
97A ASN* 3.6 7.8 - - - +
100A PRO* 3.7 13.2 - - + -
101A ARG* 3.9 12.3 - - - +
121B LYS 5.5 0.2 - - - +
129B ASN* 3.5 25.1 + - - +
130B ALA* 3.1 23.1 + - - +
132B GLY* 1.3 74.1 + - - +
134B MET* 1.3 67.6 + - - +
136B ALA* 3.3 3.1 + - - +
137B ALA* 2.9 24.8 + - - +
143B GLN* 3.4 29.6 - - - +
145B THR* 3.9 22.2 - - + +
146B PHE* 4.5 1.2 - - - -
179B THR* 4.9 3.5 - - - +
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Residues in contact with MET 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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100A PRO* 3.7 14.1 - - + +
103A ALA* 4.3 6.7 - - + -
104A ALA* 3.8 15.7 - - + +
108A VAL 4.0 21.3 - - - +
109A MET* 4.2 6.3 - - - -
110A VAL* 4.0 31.4 - - + +
98B PRO* 3.8 36.6 - - - +
99B LEU* 3.8 13.9 - - + -
102B ALA* 3.8 13.0 - - + -
130B ALA* 2.9 22.8 + - - +
131B THR 3.5 4.0 - - - +
133B GLN* 1.3 75.0 - - - +
135B LEU* 1.3 57.5 + - - +
137B ALA* 3.4 2.0 - - - +
138B ILE* 2.9 35.2 + - + +
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Residues in contact with LEU 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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6B PRO* 5.3 0.7 - - + -
102B ALA* 3.3 31.4 - - + +
105B LEU* 3.7 24.2 - - + -
106B ALA* 3.5 23.1 - - + +
117B ILE* 3.6 37.0 - - + -
119B ALA* 6.0 1.3 - - + -
131B THR* 2.8 13.0 + - + +
132B GLY* 3.2 11.2 - - - +
134B MET* 1.3 72.3 - - - +
136B ALA* 1.3 66.6 + - - +
137B ALA 3.0 2.3 + - - -
138B ILE* 3.1 3.1 + - - +
139B LEU* 2.9 41.2 + - + +
177B VAL* 4.0 8.7 - - + -
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Residues in contact with ALA 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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101A ARG* 3.7 9.4 + - - +
132B GLY 2.9 17.0 + - - +
133B GLN 3.8 3.6 - - - +
135B LEU* 1.3 71.3 - - - +
137B ALA* 1.3 52.9 + - - +
139B LEU* 3.5 0.6 + - - -
140B GLY* 2.7 30.8 + - - -
141B TRP* 2.7 18.7 + - - +
142B ALA 3.3 26.9 - - - +
143B GLN* 3.8 13.0 - - + +
177B VAL* 3.7 15.4 - - + +
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Residues in contact with ALA 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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101A ARG* 3.6 33.9 + - + +
104A ALA* 3.6 20.9 - - + -
105A LEU* 4.3 18.7 - - + +
133B GLN 2.9 17.3 + - - +
134B MET 3.4 5.8 - - - +
136B ALA* 1.3 76.9 - - - +
138B ILE* 1.3 63.9 + - - +
140B GLY* 3.0 13.5 + - - -
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Residues in contact with ILE 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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104A ALA* 4.5 12.8 - - + +
99B LEU* 4.6 7.4 - - + +
102B ALA* 3.8 14.8 - - + -
103B LYS* 3.4 49.6 - - + +
106B ALA* 3.8 22.4 - - + -
110B ARG* 4.1 10.9 + - - +
134B MET 2.9 18.7 + - - +
135B LEU* 3.7 3.6 - - - +
137B ALA* 1.3 74.4 - - - +
139B LEU* 1.3 61.3 + - + +
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Residues in contact with LEU 139 (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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106B ALA* 3.7 32.8 - - + +
109B ALA* 4.7 3.4 - - + -
110B ARG* 3.7 35.1 + - + +
117B ILE* 3.9 11.0 - - + -
135B LEU* 2.9 42.5 + - + +
136B ALA 4.0 0.7 - - - +
138B ILE* 1.3 76.7 - - - +
140B GLY* 1.3 61.5 + - - +
141B TRP* 3.5 55.5 + - + +
177B VAL* 4.3 1.1 - - + -
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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