Contacts of the strand formed by residues 3186 - 3191 (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 SER3186 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3140D LEU* 3.8 3.6 - - - +
3184D GLY 3.7 1.0 - - - -
3185D TRP* 1.3 100.4 - - - +
3187D SER* 1.3 61.9 + - - +
3200D CYS* 3.2 5.2 - - - +
3201D MET* 2.9 30.6 + - - +
3231D ARG* 3.7 2.6 - - - +
3232D THR* 3.0 27.4 + - - -
3234D GLU* 2.6 27.2 + - - -
4477D SIA 4.2 4.5 - - - -
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Residues in contact with SER3187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3127D TYR* 3.0 21.7 + - - -
3140D LEU* 4.1 7.7 - - - +
3164D LEU* 3.3 26.4 - - - +
3186D SER* 1.3 77.7 + - - +
3188D THR* 1.4 58.4 + - - +
3199D ILE 3.0 16.8 - - - -
3200D CYS* 4.0 7.4 - - - -
3232D THR* 3.4 10.6 - - - +
3234D GLU* 2.7 43.9 + - - -
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Residues in contact with THR3188 (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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3127D TYR* 3.4 8.7 + - - -
3164D LEU* 4.2 2.3 - - - +
3187D SER* 1.4 77.3 - - - +
3189D SER* 1.3 68.2 + - - +
3198D SER* 3.7 0.2 - - - -
3199D ILE* 3.0 47.5 + - + +
3232D THR* 4.3 4.7 - - + +
3233D GLN* 3.7 16.2 + - - -
3235D SER 2.7 23.3 + - - -
3237D CYS* 3.4 20.4 + - - -
3246D VAL* 3.8 26.0 - - + -
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Residues in contact with SER3189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3127D TYR* 3.6 16.5 + - - -
3129D SER* 3.9 0.9 + - - -
3138D PHE* 3.6 10.9 - - - -
3164D LEU* 4.5 1.1 - - - -
3188D THR* 1.3 81.6 + - - +
3190D CYS* 1.3 58.5 + - - +
3196D ARG* 2.8 30.2 + - - -
3197D MET 3.0 9.5 + - - -
3198D SER* 2.9 23.6 + - - -
3235D SER 4.1 1.6 + - - -
3236D GLU* 3.1 13.9 - - - +
3237D CYS* 3.0 20.9 + - - -
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Residues in contact with CYS3190 (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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3129D SER* 4.1 3.4 - - - +
3189D SER* 1.3 71.7 + - - +
3191D HIS* 1.3 62.2 + - - +
3192D ASP 4.1 0.9 + - - -
3196D ARG* 3.4 10.5 - - - +
3197D MET* 2.8 44.2 + - - +
3236D GLU* 4.8 1.8 - - + +
3237D CYS* 2.1 68.6 - - - +
3238D VAL* 3.8 1.3 - - - +
3239D CYS* 3.6 22.7 - - - -
3244D CYS* 4.0 1.1 - - - -
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Residues in contact with HIS3191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3088D ARG* 3.4 21.6 + - - -
3091D LEU* 4.5 2.6 - - - +
3129D SER* 4.7 0.4 + - - -
3130D CYS 3.6 21.1 + - - +
3131D ASP* 3.4 22.7 - - + -
3132D PRO* 3.5 13.0 - - + +
3190D CYS* 1.3 73.6 - - - +
3192D ASP* 1.3 58.6 + - - +
3193D GLY* 2.9 49.6 + - - -
3194D MET 3.3 13.2 - - - -
3195D SER* 3.3 21.0 - - - -
3196D ARG* 3.6 18.8 - - + +
3239D CYS* 3.9 9.6 + - - +
3420D TRP* 3.4 20.6 - - + -
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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