Contacts of the strand formed by residues 3188 - 3193 (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 LEU3188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3040D ILE* 4.9 9.4 - - + -
3056D LEU* 4.0 19.3 - - + -
3057D PRO 3.3 24.7 - - - +
3058D MET* 4.0 15.9 - - - -
3059D GLY 3.7 4.0 - - - +
3060D ARG 3.5 10.8 - - - +
3062D VAL* 3.8 24.5 - - + -
3079D VAL* 4.9 3.1 - - + -
3139D ASP 2.9 13.2 + - - +
3140D VAL* 3.3 13.8 - - + -
3141D ILE 2.8 27.0 + - - +
3186D ASN 3.9 1.0 + - - -
3187D THR* 1.3 74.3 - - - +
3189D LEU* 1.3 66.3 + - - +
3190D ILE* 3.9 28.9 - - + -
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Residues in contact with LEU3189 (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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3060D ARG 3.0 9.4 + - - +
3061D ILE* 3.4 6.2 - - + +
3062D VAL* 2.9 26.9 + - - +
3129D CYS* 4.7 7.6 - - + -
3141D ILE* 3.3 21.1 - - + +
3143D VAL* 3.8 17.7 - - + -
3178D LEU* 3.8 17.5 - - + -
3182D LEU* 3.7 37.7 - - + -
3187D THR 3.8 0.2 + - - -
3188D LEU* 1.3 75.1 - - - +
3190D ILE* 1.3 76.9 + - - +
3191D PHE* 3.6 32.1 - - + -
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Residues in contact with ILE3190 (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* 3.8 23.1 - - + -
3062D VAL* 3.4 18.6 - - + +
3064D ILE* 3.6 29.8 - - + -
3076D THR* 4.0 12.8 - - - +
3079D VAL* 3.9 26.0 - - + -
3140D VAL* 4.8 6.5 - - + -
3141D ILE 2.8 10.4 + - - +
3142D VAL* 3.3 13.6 - - + +
3143D VAL 2.8 27.9 + - - +
3188D LEU* 3.9 18.4 - - + -
3189D LEU* 1.3 79.5 - - - +
3191D PHE* 1.3 68.5 + - - +
3192D ILE* 4.7 0.4 - - + +
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Residues in contact with PHE3191 (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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3061D ILE* 3.7 27.8 - - + -
3062D VAL 2.7 12.4 + - - +
3063D GLU* 3.3 3.5 - - - +
3064D ILE 2.9 26.5 + - - +
3126D LEU* 4.1 21.5 - - + -
3129D CYS* 5.6 0.2 - - - -
3143D VAL* 3.7 30.3 - - + -
3146D VAL* 3.8 18.8 - - + -
3149D LEU* 4.5 4.3 - - + -
3171D MET* 4.9 3.4 - - + -
3175D MET* 3.8 28.0 - - + -
3178D LEU* 4.4 1.3 - - + -
3189D LEU* 3.6 32.5 - - + -
3190D ILE* 1.3 72.1 - - - +
3192D ILE* 1.3 63.4 + - - +
3215D LEU* 3.7 26.0 - - + -
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Residues in contact with ILE3192 (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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3064D ILE* 3.4 7.4 - - + +
3072D LYS* 3.6 49.4 - - + +
3073D THR* 3.9 6.7 - - - -
3076D THR* 3.5 33.9 - - + +
3142D VAL* 4.4 3.4 - - + -
3143D VAL 2.9 11.1 + - - +
3144D ASP* 3.4 35.9 - - + +
3145D SER* 3.0 16.9 - - - +
3146D VAL* 2.8 28.7 + - - +
3190D ILE* 4.8 2.9 - - + -
3191D PHE* 1.3 74.5 - - - +
3193D ASN* 1.3 63.6 + - - +
3501D ALF 5.4 0.4 - - - -
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Residues in contact with ASN3193 (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* 3.1 21.4 - - - +
3064D ILE 2.8 11.0 + - - +
3065D TYR* 3.3 28.6 - - + -
3066D GLY 3.7 0.7 + - - -
3072D LYS* 3.4 12.8 - - - +
3145D SER* 4.9 0.2 - - - +
3146D VAL* 3.3 20.8 - - + +
3147D ALA 3.9 2.8 - - - +
3191D PHE 3.8 0.6 + - - -
3192D ILE* 1.3 74.4 - - - +
3194D GLN* 1.3 81.6 + - - +
3209D THR* 2.9 24.4 - - - +
3210D THR* 2.9 43.7 + - - +
3215D LEU* 4.5 1.6 - - - +
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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