Contacts of the strand formed by residues 3368 - 3371 (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 TRP3368 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3100D VAL* 3.0 41.0 + - + +
3101D ASN 3.6 23.1 - - - -
3102D SER* 4.0 2.9 - - - -
3103D TRP* 3.3 50.3 - + + -
3360D ALA* 3.4 5.4 - - - +
3361D PHE* 2.9 37.6 + - + +
3366D ASN 4.4 5.2 - - - -
3367D SER* 1.3 83.3 - - - +
3369D LEU* 1.3 63.2 + - - +
3383D MET* 3.9 27.3 - - + +
3384D LEU 3.4 6.5 - - - -
3385D LYS* 3.4 44.0 - - + +
3399D SER* 3.7 17.3 - - - -
3400D ASN* 4.9 2.7 - - - -
3401D GLN* 5.0 2.5 - - + -
3428D PRO* 6.5 0.2 - - + -
2H NAG 4.7 5.8 - - + -
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Residues in contact with LEU3369 (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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3324D LEU* 4.3 10.3 - - + -
3326D SER* 4.4 4.3 - - - -
3328D VAL* 3.9 19.3 - - + +
3330D THR* 3.8 29.2 - - + -
3360D ALA* 3.5 25.8 - - + -
3362D LEU* 3.9 9.2 - - + -
3368D TRP* 1.3 79.0 - - - +
3370D GLY* 1.3 59.8 + - - +
3382D GLU 3.9 0.5 - - - +
3383D MET* 3.5 4.4 - - - -
3384D LEU* 2.8 42.8 + - + +
3386D VAL* 3.4 26.2 - - + -
3389D ALA* 3.7 27.1 - - + -
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Residues in contact with GLY3370 (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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3307D ARG* 5.0 2.1 + - - -
3330D THR* 3.4 18.1 - - - +
3358D GLY* 5.8 0.5 - - - -
3359D PHE* 3.6 18.8 + - - +
3368D TRP 4.3 0.2 + - - -
3369D LEU* 1.3 74.1 - - - +
3371D ARG* 1.3 64.6 + - - +
3381D TYR* 3.3 19.1 + - - -
3382D GLU 3.4 8.5 - - - -
3383D MET* 3.5 16.6 - - - +
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Residues in contact with ARG3371 (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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3328D VAL* 3.6 6.2 - - - +
3329D LEU 3.0 26.1 + - - -
3330D THR* 3.8 24.9 - - + +
3334D ARG* 3.7 22.0 - - - +
3337D ASP* 3.2 32.1 + - - -
3370D GLY* 1.3 77.9 - - - +
3372D THR* 1.3 69.4 + - - +
3381D TYR* 3.5 12.8 - - - -
3382D GLU* 2.8 61.0 + - + +
3384D LEU* 3.3 25.9 - - + +
3397D PRO* 5.9 1.4 - - - +
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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