Contacts of the helix formed by residues 139 - 144 (chain C) in PDB entry 3IEQ
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 LEU 139 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.8 26.7 - - + -
12B HIS 4.1 10.8 - - - +
13B GLN* 3.7 34.1 - - + +
141B TYR* 3.9 38.8 - - + -
146B GLU* 3.9 17.5 - - + +
147B GLY* 4.3 2.9 - - - -
136C ASN* 2.8 28.2 + - - +
137C GLU* 3.1 9.6 + - + +
138C LYS* 1.3 77.2 - - - +
140C GLY* 1.3 62.5 - - - +
143C GLY* 2.9 18.7 + - - -
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Residues in contact with GLY 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B TYR* 3.7 24.9 - - - +
138C LYS 4.0 1.2 + - - -
139C LEU* 1.3 72.6 - - - +
141C TYR* 1.3 67.9 + - - -
142C LEU 3.2 0.2 - - - -
143C GLY 3.0 1.7 + - - -
144C ARG* 3.0 42.6 + - - +
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Residues in contact with TYR 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN* 3.0 21.5 + - - -
139A LEU* 3.9 33.0 - - + -
140A GLY* 3.5 35.2 - - - +
141A TYR* 6.0 5.4 - + - -
142A LEU* 5.4 1.6 - - - +
141B TYR* 6.3 3.4 - + - -
9C TYR* 3.8 11.1 + - - -
11C VAL* 4.1 10.5 - - + -
140C GLY* 1.3 71.4 - - - -
142C LEU* 1.3 99.3 + - + +
144C ARG* 3.4 10.9 + - - +
145C GLY 3.3 3.8 + - - -
146C GLU* 2.9 52.3 + - + +
147C GLY 4.4 2.0 - - - -
149C GLU* 4.8 5.3 + - - -
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 5.1 0.9 - - - +
141B TYR* 5.7 0.7 - - - +
11C VAL* 4.4 0.9 - - + -
101C ILE* 3.6 32.1 - - + +
103C GLN* 3.5 16.0 + - - +
136C ASN* 3.7 28.5 - - + +
140C GLY 3.2 0.4 - - - -
141C TYR* 1.3 99.1 - - + +
143C GLY* 1.3 57.4 + - - +
145C GLY* 3.1 17.0 + - - -
147C GLY 3.6 24.4 - - - +
148C ILE* 3.8 1.6 - - - +
149C GLU* 3.6 50.3 - - + +
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Residues in contact with GLY 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLN* 3.5 25.1 - - - +
136C ASN* 3.9 1.7 - - - +
138C LYS* 3.6 35.0 - - - +
139C LEU 2.9 23.8 + - - -
140C GLY 3.0 1.1 + - - -
142C LEU* 1.3 76.6 - - - +
144C ARG* 1.3 59.2 + - - +
145C GLY 3.2 0.7 - - - -
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Residues in contact with ARG 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 6.0 2.0 - - - +
31C ARG* 4.6 4.2 + - - -
138C LYS 5.1 4.7 - - - +
140C GLY* 3.0 32.9 + - - +
141C TYR* 3.7 16.2 - - - +
142C LEU 3.3 0.4 - - - -
143C GLY* 1.3 76.1 - - - +
145C GLY* 1.3 62.1 + - - +
146C GLU* 2.7 47.0 + - - +
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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