Contacts of the strand formed by residues 3242 - 3246 (chain C) in PDB entry 2DQZ
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 ARG3242 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3214C SER* 4.1 12.2 + - - +
3215C VAL 3.4 2.8 + - - +
3216C THR* 3.0 22.2 - - + +
3217C ILE* 2.8 30.1 + - - +
3240C PHE* 3.7 4.5 - - - -
3241C HIS* 1.3 99.9 + - + +
3243C ALA* 1.3 61.8 + - - +
3344C VAL* 4.4 0.9 - - - -
3345C PRO* 3.6 24.4 - - + +
3503C PHE* 3.1 26.5 - - + -
3504C ALA 2.6 29.4 + - - -
3505C ARG 3.7 13.9 + - - -
3506C ASN* 4.2 6.3 + - - +
3507C GLY* 3.6 13.4 - - - +
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Residues in contact with ALA3243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3217C ILE* 3.4 8.3 - - + -
3227C VAL* 3.8 7.6 - - + -
3231C VAL* 3.6 23.8 - - + -
3240C PHE* 4.4 5.2 - - + -
3242C ARG* 1.3 75.9 - - - +
3244C ILE* 1.3 58.3 + - - +
3344C VAL* 4.5 2.4 - - + +
3345C PRO 2.9 9.1 + - - +
3346C TYR* 3.3 24.1 - - + -
3347C MET 2.8 27.5 + - - -
3503C PHE* 3.3 7.6 - - - -
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Residues in contact with ILE3244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3136C MET* 4.5 5.8 - - + -
3216C THR* 4.3 10.1 - - + -
3217C ILE 3.0 6.6 + - - +
3218C PHE* 3.2 34.2 - - + -
3219C GLY 3.3 6.2 + - - -
3227C VAL* 3.8 5.5 - - - +
3243C ALA* 1.3 80.4 - - - +
3245C SER* 1.3 62.8 + - - +
3246C GLU* 3.7 29.2 - - + +
3347C MET* 3.3 28.3 - - + +
3447C TYR* 5.3 0.4 - - + -
3500C TRP* 3.8 31.6 - - + +
3503C PHE* 3.7 25.6 - - + -
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Residues in contact with SER3245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3219C GLY 4.1 2.7 - - - -
3224C GLY* 3.1 18.6 + - - -
3227C VAL* 3.5 5.4 - - - +
3228C SER* 4.1 0.2 - - - -
3244C ILE* 1.3 69.7 - - - +
3246C GLU* 1.3 61.4 + - - +
3247C SER 3.7 0.8 + - - -
3248C GLY 3.5 17.3 + - - -
3249C VAL* 4.1 8.1 - - - -
3346C TYR* 2.7 34.0 + - - -
3347C MET 2.8 10.5 + - - +
3348C VAL* 3.6 3.5 - - - +
3349C GLY 3.0 29.1 + - - +
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Residues in contact with GLU3246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3138C TRP* 4.0 10.1 - - - -
3218C PHE* 3.7 12.1 - - - +
3219C GLY 3.0 16.2 + - - +
3220C GLU* 3.1 4.7 - - - +
3221C SER 2.9 25.3 + - - -
3224C GLY* 4.4 1.2 - - - -
3244C ILE* 3.7 15.2 - - + +
3245C SER* 1.3 71.4 - - - +
3247C SER* 1.3 64.2 + - - +
3248C GLY 3.6 0.2 - - - -
3349C GLY 4.1 0.2 - - - -
3447C TYR* 3.1 23.8 - - - +
3471C GLU* 3.0 30.9 - - - +
3472C LEU* 3.7 13.3 - - - +
3475C VAL* 4.0 4.8 - - - +
3500C TRP* 3.0 32.1 + - + -
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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