Contacts of the strand formed by residues 3217 - 3223 (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 ARG3217 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131B ASP 3.0 26.9 + - - -
1132B PRO 3.4 18.9 + - - -
1133B GLN 3.8 12.3 + - - -
1134B GLY* 3.7 14.5 + - - +
1135B CYS* 6.5 0.2 - - - -
1418B ASP* 2.5 38.8 + - - +
1420B TRP* 3.6 17.7 + - - +
1421B ALA* 4.2 13.2 - - + +
1422B ASN* 4.9 4.5 - - - +
3213D TRP* 3.3 4.6 - - - -
3214D TYR 2.9 32.2 + - - +
3215D GLY 4.2 9.0 + - - +
3216D GLY* 1.3 84.0 - - - +
3218D PRO* 1.3 74.8 - - + +
3219D ILE* 3.4 11.1 - - + +
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Residues in contact with PRO3218 (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* 3.7 29.4 - - + +
1106B LEU* 3.8 20.9 - - + -
1418B ASP* 5.5 2.7 - - + +
1423B LYS* 3.5 21.7 + - - +
1455B CYS* 5.3 3.4 - - + -
3211D VAL* 4.0 12.8 - - + -
3212D VAL 3.6 6.5 - - - +
3213D TRP* 3.6 23.0 - - + -
3217D ARG* 1.3 90.0 - - + +
3219D ILE* 1.3 63.4 + - - +
3221D GLU* 5.3 1.8 - - - +
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Residues in contact with ILE3219 (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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1422B ASN* 5.8 10.3 - - + +
1423B LYS* 4.3 18.1 + - - +
3212D VAL 2.7 11.7 + - - +
3213D TRP 4.3 0.7 - - - -
3214D TYR* 3.6 36.1 - - + +
3217D ARG* 3.4 27.1 - - + +
3218D PRO* 1.3 78.2 - - - +
3220D THR* 1.3 60.7 + - - +
3221D GLU* 3.8 8.3 - - - +
3266D GLU 3.7 8.7 - - - +
3267D GLY* 3.5 26.2 - - - +
3268D LYS* 4.0 15.0 - - + -
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Residues in contact with THR3220 (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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1459B LYS* 4.3 7.2 - - - +
3211D VAL* 3.5 4.2 - - - +
3212D VAL* 2.7 42.0 + - - +
3219D ILE* 1.3 82.8 + - - +
3221D GLU* 1.3 82.0 + - - +
3222D ILE* 4.2 5.2 - - + -
3267D GLY 2.6 27.4 + - - -
3268D LYS* 3.9 6.1 - - - +
3269D ILE* 4.0 28.7 + - + +
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Residues in contact with GLU3221 (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 37.3 + - + +
1423B LYS* 5.0 5.5 + - - -
1456B GLY 4.8 1.4 - - - +
1457B SER* 2.7 32.5 + - - +
1458B LYS 4.4 1.7 + - - -
1459B LYS* 3.0 37.1 + - + +
1461B LEU* 3.7 22.2 - - + -
3210D ALA 3.1 9.4 - - - +
3211D VAL* 4.6 4.0 - - + -
3218D PRO* 5.3 1.4 - - - +
3219D ILE 3.8 9.0 + - - +
3220D THR* 1.3 87.8 + - - +
3222D ILE* 1.3 65.3 + - - +
3223D PRO* 4.3 1.8 - - - -
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Residues in contact with ILE3222 (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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1459B LYS* 5.4 0.2 - - - +
3209D SER* 3.3 3.4 - - - -
3210D ALA* 2.8 43.1 + - + +
3212D VAL* 4.1 11.9 - - + -
3220D THR* 4.2 8.7 - - + -
3221D GLU* 1.3 81.8 - - - +
3223D PRO* 1.3 77.2 - - + +
3225D TRP* 4.0 22.7 - - + -
3230D LEU* 3.6 3.7 - - + +
3248D MET* 4.2 10.1 - - + -
3262D ILE* 4.1 17.3 - - + -
3264D PHE* 3.8 28.5 - - + -
3269D ILE* 4.2 14.6 - - + -
3272D ILE* 6.0 2.0 - - + -
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Residues in contact with PRO3223 (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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1459B LYS* 4.8 14.1 - - + +
1460B ARG 4.0 22.4 - - - +
1461B LEU* 4.0 16.8 - - + -
1462B GLY 5.2 2.2 - - - +
3208D ALA 4.0 4.0 - - - +
3209D SER* 4.2 5.4 - - - -
3221D GLU 4.1 3.4 - - - +
3222D ILE* 1.3 93.5 - - + +
3224D SER* 1.3 68.7 + - - +
3225D TRP* 3.5 15.4 + - - +
3230D LEU* 4.2 1.1 - - - -
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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