Contacts of the strand formed by residues 3188 - 3193 (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 LEU3188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3040A ILE* 4.9 9.2 - - + -
3056A LEU* 4.0 19.3 - - + +
3057A PRO 3.3 24.5 - - - +
3058A MET* 4.0 17.5 - - - -
3059A GLY 3.6 3.8 - - - +
3060A ARG 3.5 14.6 - - - +
3062A VAL* 3.8 24.0 - - + -
3079A VAL* 4.9 3.6 - - + -
3139A ASP 2.9 12.3 + - - +
3140A VAL* 3.3 13.5 - - + -
3141A ILE 2.9 26.5 + - - +
3186A ASN 3.9 1.0 + - - -
3187A THR* 1.3 74.4 - - - +
3189A LEU* 1.3 61.1 + - - +
3190A ILE* 3.9 28.7 - - + -
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Residues in contact with LEU3189 (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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3060A ARG 3.0 9.4 + - - +
3061A ILE* 3.4 6.0 - - + +
3062A VAL 2.9 26.3 + - - +
3129A CYS* 4.7 7.6 - - + -
3141A ILE* 3.3 21.3 - - + +
3143A VAL* 3.8 17.0 - - + -
3178A LEU* 3.8 17.3 - - + -
3182A LEU* 3.7 37.2 - - + -
3187A THR 3.8 0.6 + - - -
3188A LEU* 1.3 74.1 - - - +
3190A ILE* 1.3 75.6 + - - +
3191A PHE* 3.6 35.7 - - + -
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Residues in contact with ILE3190 (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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3056A LEU* 3.8 22.2 - - + -
3062A VAL* 3.3 18.2 - - + +
3064A ILE* 3.7 29.8 - - + -
3076A THR* 4.0 13.0 - - - +
3079A VAL* 3.9 26.5 - - + -
3140A VAL* 4.7 7.0 - - + -
3141A ILE 2.8 10.3 + - - +
3142A VAL* 3.3 13.8 - - + +
3143A VAL 2.8 27.7 + - - +
3188A LEU* 3.9 18.2 - - + -
3189A LEU* 1.3 79.1 - - - +
3191A PHE* 1.3 68.2 + - - +
3192A ILE* 4.0 1.1 + - + +
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Residues in contact with PHE3191 (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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3061A ILE* 3.7 17.0 - - + -
3062A VAL 2.7 11.9 + - - +
3063A GLU* 3.2 3.3 - - - +
3064A ILE 2.9 26.9 + - - +
3126A LEU* 4.1 22.2 - - + -
3143A VAL* 3.8 30.7 - - + -
3146A VAL* 3.8 19.3 - - + -
3149A LEU* 4.5 3.8 - - + -
3171A MET* 4.8 3.1 - - + -
3175A MET* 3.8 29.6 - - + -
3178A LEU* 4.4 1.3 - - + -
3189A LEU* 3.6 32.1 - - + -
3190A ILE* 1.3 73.7 - - - +
3192A ILE* 1.3 62.1 + - - +
3215A LEU* 3.7 33.7 - - + -
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Residues in contact with ILE3192 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3064A ILE* 3.4 7.6 - - + +
3072A LYS* 3.6 49.4 - - + +
3073A THR* 3.9 5.2 - - - -
3076A THR* 3.4 32.3 - - + +
3142A VAL* 4.4 3.6 - - + -
3143A VAL 2.9 11.0 + - - +
3144A ASP* 3.4 37.5 - - + +
3145A SER* 3.0 17.1 - - - +
3146A VAL* 2.8 27.9 + - - +
3190A ILE* 4.8 3.4 - - + -
3191A PHE* 1.3 75.5 - - - +
3193A ASN* 1.3 62.4 + - - +
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Residues in contact with ASN3193 (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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3063A GLU* 3.1 20.8 - - + +
3064A ILE 2.8 8.0 + - - +
3065A TYR* 3.3 29.5 - - + -
3066A GLY 3.7 0.3 + - - -
3072A LYS* 3.4 13.3 - - - +
3145A SER* 4.9 0.4 - - - +
3146A VAL* 3.3 21.5 - - + +
3147A ALA 3.9 2.8 - - - +
3191A PHE 3.8 0.2 + - - -
3192A ILE* 1.3 75.3 - - - +
3194A GLN* 1.3 82.0 + - - +
3209A THR* 2.9 14.9 - - - +
3210A THR* 2.9 52.9 + - - +
3215A LEU* 4.5 1.7 - - - +
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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