Contacts of the strand formed by residues 3244 - 3250 (chain D) in PDB entry 1W21
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 CYS3244 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3190D CYS* 4.0 4.9 - - - -
3192D ASP* 3.9 13.0 - - - -
3197D MET* 3.8 27.1 - - + -
3214D TYR* 6.3 0.9 - - - -
3238D VAL 3.4 4.7 - - - +
3239D CYS* 2.0 48.0 - - - -
3242D GLY 4.1 5.4 - - - -
3243D VAL* 1.3 72.2 - - - +
3245D PRO* 1.3 67.1 - - - +
3246D VAL* 4.0 0.7 - - - +
3262D ILE 3.7 1.4 - - - +
3264D PHE* 2.8 41.0 + - + +
3265D LYS* 5.8 0.2 - - - -
3266D GLU 6.0 1.1 - - - -
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Residues in contact with PRO3245 (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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3233D GLN* 4.4 2.1 + - - -
3237D CYS* 3.6 13.9 - - - +
3238D VAL 3.1 17.9 + - - +
3243D VAL* 3.5 9.6 - - + +
3244D CYS* 1.3 86.9 - - - +
3246D VAL* 1.3 64.4 + - - +
3247D VAL* 5.9 0.2 - - - -
3261D ILE* 4.2 2.7 - - + -
3262D ILE 3.5 7.2 - - - +
3263D TYR* 3.7 35.0 - - + -
3287D CYS* 6.1 0.5 - - - -
3294D ILE* 3.8 17.3 - - + -
3312D ILE* 3.9 31.6 - - + -
3314D PRO* 4.5 7.2 - - + -
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Residues in contact with VAL3246 (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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3188D THR* 3.8 13.9 - - + -
3197D MET* 3.7 30.3 - - + -
3199D ILE* 3.9 4.3 - - + -
3232D THR* 3.6 21.1 - - - +
3233D GLN* 3.6 6.5 - - - +
3237D CYS* 4.0 10.3 - - + -
3245D PRO* 1.3 79.5 - - - +
3247D VAL* 1.3 65.7 + - - +
3248D MET* 3.9 21.1 + - + +
3260D LYS 3.8 0.5 - - - +
3261D ILE* 3.4 3.9 - - - -
3262D ILE* 2.9 36.7 + - - +
3264D PHE* 3.8 15.5 - - + -
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Residues in contact with VAL3247 (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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3232D THR* 2.8 23.6 + - - -
3233D GLN* 2.9 28.0 + - - +
3246D VAL* 1.3 74.2 - - - +
3248D MET* 1.3 63.8 + - - +
3249D THR* 5.0 0.2 - - - +
3259D THR* 3.8 13.9 - - + -
3260D LYS 3.7 4.5 - - - +
3261D ILE* 4.5 11.7 - - + +
3282D ILE* 3.8 16.4 - - + -
3285D CYS* 3.7 33.4 - - + +
3296D CYS* 4.1 16.4 - - - -
3310D ILE* 4.1 11.7 - - + -
3312D ILE* 4.5 7.9 - - + -
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Residues in contact with MET3248 (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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3199D ILE* 4.3 13.0 - - + -
3201D MET* 3.7 28.3 - - + -
3210D ALA* 5.0 2.5 - - + -
3222D ILE* 4.2 12.6 - - + -
3225D TRP* 3.7 29.8 - - + -
3230D LEU* 4.5 1.6 - - + -
3231D ARG 3.3 9.2 - - - +
3232D THR* 4.0 4.3 - - - +
3246D VAL* 3.9 22.9 - - + +
3247D VAL* 1.3 78.0 - - - +
3249D THR* 1.3 68.3 + - - +
3259D THR* 3.2 4.2 - - - +
3260D LYS* 2.8 35.0 + - + +
3262D ILE* 4.1 13.7 - - + -
3264D PHE* 4.0 26.2 - - + -
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Residues in contact with THR3249 (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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3225D TRP* 4.5 0.2 - - - -
3230D LEU* 3.5 3.1 - - - +
3231D ARG* 2.8 56.5 + - - +
3247D VAL* 5.0 0.7 - - - +
3248D MET* 1.3 76.6 + - - +
3250D ASP* 1.3 62.9 + - - +
3257D ALA* 4.0 23.8 - - + -
3258D ALA 3.7 5.2 - - - +
3259D THR* 2.9 20.2 + - - +
3281D HIS* 5.3 0.9 - - + -
3282D ILE* 2.7 32.1 + - - +
3283D GLU* 4.3 10.6 - - - -
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Residues in contact with ASP3250 (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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3224D SER* 2.6 26.2 + - - -
3225D TRP* 2.8 38.6 + - + +
3226D ALA* 2.9 11.2 + - - +
3227D GLY 3.5 0.3 + - - -
3228D ASN 2.8 40.6 + - - +
3230D LEU* 3.8 13.6 - - + +
3231D ARG* 4.2 0.7 - - - +
3249D THR* 1.3 78.2 - - - +
3251D GLY* 1.3 58.3 + - - +
3258D ALA* 2.9 33.8 + - - +
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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