Contacts of the strand formed by residues 3061 - 3065 (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 ILE3061 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3060A ARG* 1.3 73.9 - - - +
3062A VAL* 1.3 65.2 + - - +
3175A MET* 4.1 11.9 - - - -
3178A LEU* 4.9 3.6 - - + -
3179A ALA* 4.4 20.9 - - + +
3182A LEU* 3.7 29.4 - - + -
3189A LEU* 3.4 7.9 - - + +
3191A PHE* 3.7 18.6 - - + -
3215A LEU* 3.7 28.3 - - + -
3218A TYR* 4.1 31.3 + - + +
3219A ALA* 3.3 4.6 - - - +
3220A SER* 2.7 35.1 + - - -
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Residues in contact with VAL3062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3056A LEU* 3.9 27.1 - - + -
3057A PRO* 4.1 10.3 - - + -
3060A ARG 5.1 0.2 - - - -
3061A ILE* 1.3 84.4 - - - +
3063A GLU* 1.3 64.9 + - - +
3064A ILE* 4.6 6.1 - - + -
3188A LEU* 3.8 20.0 - - + -
3189A LEU 2.9 9.5 + - - +
3190A ILE* 3.3 18.7 - - + -
3191A PHE* 2.7 34.5 + - - +
3219A ALA* 4.6 0.7 - - - -
3221A VAL* 3.4 30.3 - - + +
3223A LEU* 4.6 1.3 - - + -
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Residues in contact with GLU3063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3062A VAL* 1.3 75.6 - - - +
3064A ILE* 1.3 64.4 + - - +
3065A TYR* 4.3 5.1 - - + -
3191A PHE 3.2 9.4 - - - +
3193A ASN* 3.1 31.3 - - + +
3209A THR* 3.2 15.6 + - - +
3215A LEU* 3.5 34.7 - - + +
3216A LYS 4.6 0.2 + - - -
3219A ALA* 4.3 2.2 - - + +
3221A VAL 3.0 7.3 + - - +
3222A ARG* 2.4 47.7 + - - +
3223A LEU* 2.7 32.4 + - - +
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Residues in contact with ILE3064 (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* 5.6 1.3 - - + -
3062A VAL* 4.6 2.9 - - + -
3063A GLU* 1.3 77.9 - - - +
3065A TYR* 1.3 63.3 + - - +
3072A LYS* 4.3 14.6 - - + +
3075A LEU* 3.7 30.1 - - + -
3076A THR* 4.1 11.2 - - - +
3190A ILE* 3.7 29.8 - - + -
3191A PHE 2.9 8.5 + - - +
3192A ILE* 3.4 10.7 - - + +
3193A ASN 2.8 25.7 + - - +
3223A LEU* 3.4 30.5 - - + +
3225A ILE* 3.8 27.1 - - + -
3244A VAL* 6.2 0.2 - - + -
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Residues in contact with TYR3065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3063A GLU* 4.3 7.9 - - + -
3064A ILE* 1.3 75.4 - - - +
3066A GLY* 1.3 64.2 + - - +
3072A LYS* 3.9 4.9 - - - -
3193A ASN* 3.3 20.6 - - + +
3194A GLN 4.8 2.5 - - - +
3195A ILE* 4.3 11.2 - - + -
3207A GLU* 5.4 1.8 - - - -
3209A THR* 3.9 19.7 - - - +
3222A ARG* 3.7 41.6 + - + -
3223A LEU 2.8 19.1 + - - +
3224A ASP* 3.5 29.0 + - + -
3225A ILE* 2.9 27.0 + - - +
3226A ARG* 4.6 5.4 - - - -
3247A VAL* 3.5 27.7 - - + +
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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
------------------------------------------------------------
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