Contacts of the strand formed by residues 3283 - 3290 (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 GLU3283 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3231D ARG* 2.4 48.0 + - - +
3249D THR* 4.3 4.8 - - - -
3253D ALA* 4.1 0.9 - - - -
3281D HIS* 3.5 21.0 + - + +
3282D ILE* 1.4 84.4 - - - +
3284D GLU* 1.3 73.2 + - + +
3285D CYS* 3.1 3.8 + - - -
3298D CYS* 3.3 3.2 - - - +
3299D ARG* 2.8 48.7 + - + +
3301D ASN* 3.9 7.4 - - + +
4477D SIA 2.7 32.8 + - - +
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Residues in contact with GLU3284 (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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3231D ARG* 6.5 1.8 - - + -
3232D THR 3.9 14.6 + - - +
3233D GLN* 3.2 17.0 - - - +
3234D GLU* 3.8 16.9 - - + +
3283D GLU* 1.3 76.8 + - + +
3285D CYS* 1.3 64.6 + - - +
3286D SER* 3.5 1.6 + - - -
3297D ILE 4.3 2.3 - - - +
3298D CYS* 4.4 1.9 - - - -
3299D ARG* 2.8 33.4 + - + -
3357D LYS* 3.0 34.7 + - + +
3358D GLY 4.7 0.7 - - - +
3412D TYR* 2.4 34.5 + - - -
4477D SIA 3.3 24.4 + - - +
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Residues in contact with CYS3285 (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* 3.1 41.2 - - + +
3235D SER* 3.3 6.4 + - - -
3247D VAL* 3.7 21.1 - - + +
3282D ILE* 3.5 19.7 - - - -
3283D GLU 3.1 1.6 + - - -
3284D GLU* 1.3 76.0 - - - +
3286D SER* 1.3 59.7 + - - +
3287D CYS* 3.9 2.9 - - - -
3296D CYS* 3.9 11.4 - - + -
3297D ILE 3.8 1.1 - - - -
3298D CYS* 2.1 48.2 - - - -
3310D ILE* 4.0 1.8 - - - -
3357D LYS* 3.3 1.2 + - - -
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Residues in contact with SER3286 (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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3235D SER* 3.5 6.1 - - - -
3284D GLU 3.5 0.2 + - - -
3285D CYS* 1.3 70.5 - - - +
3287D CYS* 1.3 59.3 + - - +
3288D TYR* 5.2 0.9 - - - -
3295D LYS 3.8 1.0 - - - +
3296D CYS* 3.4 0.2 - - - -
3297D ILE* 2.8 38.8 + - - +
3357D LYS* 2.8 24.0 + - - -
3358D GLY 2.6 28.1 + - - -
3359D PHE* 3.5 17.7 - - - +
3360D ALA 5.4 0.3 - - - +
3414D GLY* 3.5 5.1 - - - -
3415D ALA* 3.8 15.1 - - - +
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Residues in contact with CYS3287 (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* 3.7 29.4 - - - +
3235D SER* 4.5 0.4 + - - -
3236D GLU* 4.1 18.1 + - - +
3237D CYS* 5.2 1.3 - - - -
3238D VAL* 3.6 21.1 - - + +
3245D PRO 6.1 0.4 - - - -
3285D CYS* 3.9 4.8 + - - -
3286D SER* 1.3 74.9 - - - +
3288D TYR* 1.3 63.9 + - - +
3294D ILE* 4.2 4.0 - - + -
3295D LYS 3.0 4.5 - - - +
3296D CYS* 2.1 48.7 - - - -
3415D ALA* 4.1 16.9 + - - +
3416D PHE* 5.1 0.2 - - - -
3419D TYR* 4.7 0.3 + - - -
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Residues in contact with TYR3288 (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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3097D LEU* 4.0 24.2 - - + +
3238D VAL* 3.7 8.1 - - - -
3286D SER 5.2 0.4 - - - -
3287D CYS* 1.3 77.8 - - - +
3289D GLY* 1.3 68.1 + - - +
3290D ALA* 4.6 7.9 - - + -
3293D VAL 3.9 1.0 - - - +
3294D ILE* 3.4 2.9 - - - -
3295D LYS* 3.0 61.9 + - + +
3297D ILE* 4.4 4.5 - - + -
3360D ALA 3.5 23.1 - - - -
3361D PHE* 3.6 35.0 - + + -
3362D LEU* 2.7 39.5 + - - -
3415D ALA* 4.6 5.6 - - + -
3416D PHE 5.6 0.9 - - - +
3417D ILE* 3.9 6.3 - - + -
3419D TYR* 3.3 13.5 - - - +
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Residues in contact with GLY3289 (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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3093D LEU* 4.0 21.1 - - - -
3238D VAL* 4.0 3.3 - - - +
3288D TYR* 1.3 82.5 - - - +
3290D ALA* 1.3 64.7 + - - +
3293D VAL 3.5 7.9 - - - -
3294D ILE* 4.4 0.7 - - - -
3417D ILE* 4.2 3.8 - - - +
3419D TYR* 2.8 33.3 + - - -
3426D PHE* 3.5 7.0 - - - -
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Residues in contact with ALA3290 (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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3093D LEU* 4.5 2.8 - - - +
3095D LYS 3.4 12.6 - - - +
3096D PRO* 4.3 1.8 - - + -
3097D LEU* 3.9 33.9 - - + +
3288D TYR* 4.6 6.9 - - + -
3289D GLY* 1.3 77.4 - - - +
3291D GLY* 1.3 68.2 + - - +
3292D GLY 3.2 2.5 - - - -
3293D VAL* 3.1 22.8 + - - +
3426D PHE* 4.1 4.5 - - + -
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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