Contacts of the strand formed by residues 3308 - 3313 (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 PRO3308 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3279D ALA* 3.8 10.5 - - + -
3281D HIS 3.5 22.2 - - - +
3282D ILE* 3.4 24.9 - - + -
3296D CYS 4.5 0.2 - - - -
3297D ILE* 3.7 1.6 - - - -
3298D CYS* 3.0 42.5 + - + +
3299D ARG 4.3 1.3 - - - -
3300D ASP* 3.6 27.4 - - + +
3306D ASN 3.8 1.1 - - - +
3307D ARG* 1.3 87.2 - - - +
3309D VAL* 1.3 61.5 + - - +
3310D ILE 4.3 0.2 - - - -
3322D LYS 3.4 7.2 - - - +
3323D TYR* 3.8 11.4 - - + -
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Residues in contact with VAL3309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3295D LYS* 5.1 3.1 - - + -
3296D CYS 3.4 9.4 - - - +
3297D ILE* 4.4 10.1 - - + -
3308D PRO* 1.3 78.6 - - - +
3310D ILE* 1.3 73.0 + - - +
3311D THR* 4.2 6.6 + - - +
3321D SER* 3.2 3.2 - - - -
3322D LYS* 2.8 41.8 + - + +
3323D TYR 4.2 2.2 - - - -
3324D LEU* 3.7 44.2 - - + +
3362D LEU* 4.1 20.4 - - + -
3390D GLU* 4.3 13.5 - - + +
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Residues in contact with ILE3310 (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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3247D VAL* 4.1 13.9 - - + -
3261D ILE* 3.8 25.6 - - + -
3275D LEU* 4.0 13.5 - - + -
3282D ILE* 3.9 40.2 - - + -
3285D CYS* 4.0 12.3 - - - -
3294D ILE 3.9 0.7 - - - +
3295D LYS* 3.6 3.1 - - - -
3296D CYS* 2.9 38.5 + - + +
3298D CYS* 4.2 4.0 - - - -
3309D VAL* 1.3 76.5 - - - +
3311D THR* 1.3 63.3 + - - +
3312D ILE* 3.9 11.8 + - + +
3319D HIS* 4.0 7.2 - - + -
3320D THR 3.4 13.2 - - - +
3321D SER* 4.2 8.5 - - - -
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Residues in contact with THR3311 (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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3293D VAL* 3.6 25.6 - - + -
3294D ILE 3.6 3.4 - - - +
3295D LYS* 4.7 8.1 - - + +
3309D VAL* 4.2 7.7 + - - +
3310D ILE* 1.3 72.9 - - - +
3312D ILE* 1.3 65.2 + - - +
3313D ASP 4.3 0.2 + - - -
3319D HIS* 3.1 5.9 - - - +
3320D THR* 3.0 44.1 + - - +
3390D GLU* 4.4 13.0 + - - -
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Residues in contact with ILE3312 (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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3245D PRO* 3.9 29.6 - - + -
3247D VAL* 4.5 5.4 - - + -
3261D ILE* 4.0 19.5 - - + -
3263D TYR* 3.8 29.6 - - + +
3293D VAL* 3.9 3.9 - - - +
3294D ILE* 2.8 47.2 + - + +
3296D CYS* 4.1 22.9 - - - -
3310D ILE* 3.9 16.8 - - + +
3311D THR* 1.3 79.6 - - - +
3313D ASP* 1.3 65.0 + - - +
3314D PRO* 3.1 7.4 - - + +
3318D THR 3.6 7.2 - - - +
3319D HIS* 4.1 5.4 - - + -
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Residues in contact with ASP3313 (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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3292D GLY 4.9 2.8 - - - +
3293D VAL* 5.6 1.3 - - - +
3311D THR 4.3 0.4 + - - -
3312D ILE* 1.3 73.0 - - - +
3314D PRO* 1.3 56.7 - - - +
3315D GLU* 3.0 10.6 + - - +
3316D MET* 2.9 39.4 + - - +
3317D MET* 2.8 35.9 + - - -
3318D THR* 2.9 22.9 + - - +
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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