Contacts of the helix formed by residues 3151 - 3157 (chain A) in PDB entry 3CMT
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 PRO3151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3123A GLU* 3.5 17.5 - - - +
3149A LEU 3.3 9.6 - - - +
3150A THR* 1.3 88.4 - - - +
3152A LYS* 1.3 64.9 + - - +
3154A GLU* 3.1 34.8 + - + +
3155A ILE* 3.1 10.9 + - - +
3163A HIS* 6.2 0.4 - - + -
3166A LEU* 3.8 28.0 - - + -
3167A ALA* 3.8 35.9 - - + +
3170A MET* 4.4 7.2 - - - -
4176A ARG* 4.9 1.8 - - - +
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Residues in contact with LYS3152 (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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3121A THR* 3.9 28.5 - - + +
3123A GLU* 2.7 27.3 + - + +
3150A THR 3.6 0.2 + - - -
3151A PRO* 1.3 72.8 - - - +
3153A ALA* 1.3 57.8 + - - +
3155A ILE* 3.2 3.5 + - - +
3156A GLU* 3.0 64.9 + - + +
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Residues in contact with ALA3153 (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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3151A PRO* 3.3 1.0 - - - +
3152A LYS* 1.3 79.5 - - - +
3154A GLU* 1.3 52.5 + - - +
3156A GLU* 4.2 6.9 - - - +
3157A GLY* 2.8 31.5 + - - -
3163A HIS* 3.7 12.9 - - + +
3166A LEU* 3.8 22.7 - - + -
2009C T 6.2 0.2 - - - +
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Residues in contact with GLU3154 (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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3150A THR* 3.6 12.3 - - + +
3151A PRO* 3.1 32.9 + - + +
3153A ALA* 1.3 76.5 - - - +
3155A ILE* 1.3 64.3 + - - +
3157A GLY 3.3 11.6 + - - +
3158A GLU 4.6 0.7 - - - +
3163A HIS* 3.3 33.9 + - + +
4173A GLN* 3.0 35.9 - - + +
4176A ARG* 2.8 36.7 + - - -
4177A LYS* 3.3 23.4 - - + +
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Residues in contact with ILE3155 (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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3120A ASP* 3.1 30.1 - - + +
3121A THR* 3.8 15.0 - - + -
3150A THR* 3.6 40.2 - - + +
3151A PRO 3.1 6.0 + - - +
3152A LYS* 3.6 8.1 - - + +
3154A GLU* 1.3 76.5 - - - +
3156A GLU* 1.3 65.8 + - + +
3157A GLY 3.4 1.2 - - - +
4130A ASP* 5.1 0.9 - - - +
4134A ARG* 5.6 1.9 + - - -
4176A ARG 5.6 0.7 - - - +
4177A LYS* 3.3 32.3 + - + +
4181A ASN* 6.0 4.3 - - - +
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Residues in contact with GLU3156 (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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3152A LYS* 3.0 57.2 + - + +
3153A ALA* 4.2 5.4 + - - +
3155A ILE* 1.3 78.0 - - + +
3157A GLY* 1.3 65.6 + - - +
3158A GLU* 5.7 0.5 - - - +
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Residues in contact with GLY3157 (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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3153A ALA 2.8 19.9 + - - -
3154A GLU 3.3 4.9 - - - +
3155A ILE 3.3 1.0 - - - +
3156A GLU* 1.3 81.9 - - - +
3158A GLU* 1.3 58.7 + - - +
3161A ASP* 3.5 9.6 - - - -
3163A HIS* 4.7 4.3 - - - -
4177A LYS* 2.7 29.3 + - - -
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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