Contacts of the strand formed by residues 3209 - 3214 (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 SER3209 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104B HIS* 5.9 0.7 - - - +
1461B LEU* 4.2 32.0 - - - +
1462B GLY 4.5 12.2 + - - -
3200D CYS 3.8 0.9 - - - +
3201D MET* 3.3 2.9 - - - -
3202D SER* 3.0 34.7 + - - -
3207D ASN 5.0 0.2 + - - -
3208D ALA* 1.3 75.3 - - - +
3210D ALA* 1.3 62.4 + - - +
3211D VAL* 5.2 6.3 - - - +
3222D ILE 3.3 12.3 - - - -
3223D PRO* 4.2 2.9 - - - -
3230D LEU* 4.0 5.8 - - - -
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Residues in contact with ALA3210 (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* 4.0 12.8 - - + -
3200D CYS 3.3 5.2 - - - +
3201D MET* 3.8 29.4 - - + -
3209D SER* 1.3 75.3 - - - +
3211D VAL* 1.3 63.2 + - - +
3212D VAL* 4.1 0.7 - - + -
3221D GLU* 3.1 7.3 - - - +
3222D ILE* 2.8 58.3 + - + +
3230D LEU* 3.7 3.5 - - + +
3248D MET* 5.0 1.1 - - + -
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Residues in contact with VAL3211 (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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1104B HIS* 3.9 41.1 - - + +
1105B ILE* 4.0 20.0 - - + +
1461B LEU* 5.7 0.2 - - + -
3182D CYS* 5.8 0.7 - - + -
3183D ILE 5.9 0.9 - - - +
3199D ILE* 3.4 4.6 - - - -
3200D CYS* 3.0 31.0 + - + +
3202D SER* 6.1 0.2 - - - +
3209D SER* 5.2 7.6 - - - +
3210D ALA* 1.3 77.9 - - - +
3212D VAL* 1.3 62.2 + - - +
3213D TRP* 3.2 32.2 - - + +
3218D PRO* 4.0 14.4 - - + -
3220D THR 3.5 7.9 - - - +
3221D GLU* 4.6 3.6 - - + -
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Residues in contact with VAL3212 (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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3197D MET* 3.9 20.9 - - + -
3198D SER 3.7 2.5 - - - -
3199D ILE* 4.0 17.3 - - + -
3211D VAL* 1.3 75.0 - - - +
3213D TRP* 1.3 57.2 + - - +
3218D PRO* 3.6 2.3 - - - +
3219D ILE* 2.7 32.6 + - - +
3220D THR* 2.7 26.9 + - - +
3222D ILE* 4.1 14.8 - - + -
3264D PHE* 3.8 28.5 - - + -
3267D GLY* 3.7 28.9 - - - +
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Residues in contact with TRP3213 (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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1105B ILE 4.4 3.8 + - - -
1106B LEU* 3.2 55.0 - - + -
1169B MET* 3.8 18.2 - - + -
3180D VAL 6.0 0.9 - - - -
3181D GLU 3.7 15.7 - - - +
3182D CYS* 3.4 28.3 - - + +
3183D ILE 5.1 0.9 - - - +
3196D ARG 4.4 0.4 - - - -
3197D MET* 3.1 11.5 - - - +
3198D SER* 2.6 46.2 + - - +
3211D VAL* 3.2 35.2 - - + +
3212D VAL* 1.3 77.0 - - - +
3214D TYR* 1.3 60.3 + - - +
3216D GLY* 3.5 35.2 - - - -
3217D ARG 3.3 4.9 - - - +
3218D PRO* 3.6 20.2 - - + -
3219D ILE* 4.3 0.7 - - - -
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Residues in contact with TYR3214 (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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3090D PHE* 4.2 1.6 - - - -
3192D ASP* 2.5 36.3 + - + -
3194D MET* 3.9 8.0 - - - +
3195D SER* 3.5 32.9 + - - -
3196D ARG 3.3 14.6 - - - -
3197D MET* 4.1 12.1 - - + -
3213D TRP* 1.3 74.3 - - - +
3215D GLY* 1.3 67.6 + - - +
3216D GLY 3.1 0.7 + - - -
3217D ARG* 2.9 23.8 + - - +
3219D ILE* 3.6 22.9 - - + +
3244D CYS* 6.3 0.9 - - - -
3266D GLU* 3.7 54.9 + - + +
3267D GLY 4.1 1.8 - - - +
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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