Contacts of the strand formed by residues 3061 - 3065 (chain D) 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 ILE3061 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3060D ARG* 1.3 75.1 - - - +
3062D VAL* 1.3 65.6 + - - +
3175D MET* 4.1 12.1 - - - +
3178D LEU* 4.9 3.1 - - + -
3179D ALA* 4.4 20.6 - - + +
3182D LEU* 3.7 28.5 - - + -
3189D LEU* 3.4 7.9 - - + +
3191D PHE* 3.7 29.4 - - + -
3215D LEU* 3.7 17.5 - - + -
3218D TYR* 4.1 32.4 + - + +
3219D ALA* 3.3 4.4 - - - -
3220D SER* 2.7 34.1 + - - -
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Residues in contact with VAL3062 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3056D LEU* 3.9 28.3 - - + -
3057D PRO* 4.0 10.5 - - + -
3060D ARG 5.1 0.2 - - - -
3061D ILE* 1.3 85.1 - - - +
3063D GLU* 1.3 66.5 + - - +
3064D ILE* 4.6 6.3 - - + -
3188D LEU* 3.8 19.5 - - + -
3189D LEU 2.9 9.8 + - - +
3190D ILE* 3.4 19.7 - - + +
3191D PHE* 2.7 34.8 + - - +
3219D ALA* 4.7 0.2 - - - -
3221D VAL* 3.4 29.2 - - + +
3223D LEU* 4.6 0.7 - - + -
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Residues in contact with GLU3063 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3062D VAL* 1.3 76.1 - - - +
3064D ILE* 1.3 66.5 + - - +
3065D TYR* 4.3 6.0 - - + -
3191D PHE 3.3 8.5 - - - +
3193D ASN* 3.1 31.9 - - + +
3209D THR* 3.2 15.8 + - - +
3215D LEU* 3.5 33.9 - - + +
3216D LYS 4.6 0.2 + - - -
3219D ALA* 4.3 2.6 - - + +
3221D VAL 3.0 7.8 + - - +
3222D ARG* 2.5 47.3 + - - +
3223D LEU* 2.7 32.9 + - - +
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Residues in contact with ILE3064 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3056D LEU* 5.6 1.3 - - + -
3062D VAL* 4.6 3.1 - - + -
3063D GLU* 1.3 78.4 - - - +
3065D TYR* 1.3 63.0 + - - +
3072D LYS* 4.3 14.4 - - + +
3075D LEU* 3.7 30.3 - - + -
3076D THR* 4.1 10.8 - - - +
3190D ILE* 3.6 28.7 - - + -
3191D PHE 2.9 8.5 + - - +
3192D ILE* 3.4 11.2 - - + +
3193D ASN 2.8 26.1 + - - +
3223D LEU* 3.4 29.8 - - + +
3225D ILE* 3.8 28.0 - - + -
3244D VAL* 6.1 0.2 - - + -
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Residues in contact with TYR3065 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3063D GLU* 4.3 8.1 - - + -
3064D ILE* 1.3 75.1 - - - +
3066D GLY* 1.3 63.8 + - - +
3072D LYS* 3.9 5.4 - - - -
3193D ASN* 3.3 26.5 - - + +
3194D GLN 4.8 2.0 - - - +
3195D ILE* 4.3 11.9 - - + -
3207D GLU* 5.4 2.0 - - - -
3208D THR 5.9 0.2 - - - -
3209D THR* 3.9 13.7 - - - +
3222D ARG* 3.7 41.7 + - + -
3223D LEU 2.9 18.0 + - - +
3224D ASP* 3.5 28.8 + - + -
3225D ILE* 2.9 26.8 + - - +
3226D ARG* 4.6 4.5 - - - -
3247D VAL* 3.5 27.9 - - + +
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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