Contacts of the strand formed by residues 3447 - 3457 (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 THR3447 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3122D VAL* 3.2 22.1 - - - +
3123D THR 4.0 2.1 - - - +
3124D ARG* 3.9 27.3 - - + +
3142D GLN* 5.2 0.5 + - - +
3154D THR* 3.0 11.7 + - - +
3155D ILE* 3.4 30.2 - - + +
3435D ILE* 4.3 6.5 - - + -
3436D ARG 3.6 7.2 - - - +
3438D ARG* 2.8 39.8 + - - +
3446D TRP* 1.3 72.3 - - - +
3448D SER* 1.3 63.9 + - - +
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Residues in contact with SER3448 (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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3112D ILE* 3.8 19.7 - - - +
3121D LEU 4.3 2.4 + - - -
3122D VAL* 3.6 12.3 - - - -
3123D THR* 3.2 30.2 + - - -
3124D ARG* 4.4 2.4 - - - +
3146D LEU* 4.0 15.5 - - - +
3435D ILE* 3.3 8.1 - - - +
3436D ARG 2.8 29.5 + - - +
3446D TRP* 3.7 2.1 - - - -
3447D THR* 1.3 77.9 - - - +
3449D ASN* 1.3 73.7 + - - +
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Residues in contact with ASN3449 (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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3111D ALA* 3.9 9.7 - - - +
3112D ILE* 3.8 16.3 - - - +
3123D THR* 2.6 53.3 + - - -
3124D ARG* 3.1 10.8 - - + +
3126D PRO* 3.5 17.5 - - - +
3173D PRO* 5.9 0.2 - - - +
3433D GLU* 3.7 25.6 - - + +
3434D LEU 3.2 14.1 - - - +
3435D ILE* 4.1 1.1 - - - -
3448D SER* 1.3 84.0 + - - +
3450D SER* 1.3 73.6 + - - +
3451D ILE* 3.8 4.7 - - - +
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Residues in contact with SER3450 (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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3108D LYS* 4.6 2.6 + - - -
3109D ASP* 3.6 11.7 - - - -
3110D ASN* 4.4 2.9 - - - -
3111D ALA* 3.7 20.0 - - - -
3112D ILE* 4.1 1.3 - - - +
3433D GLU* 3.9 1.2 - - - -
3434D LEU* 3.0 47.4 + - - +
3449D ASN* 1.3 82.0 - - - +
3451D ILE* 1.3 68.3 + - - +
3468D ASP* 2.9 28.4 + - - -
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Residues in contact with ILE3451 (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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3108D LYS* 3.2 9.4 - - - +
3109D ASP* 2.7 44.5 + - - +
3126D PRO* 3.7 31.6 - - + -
3127D TYR 4.9 1.8 - - - +
3128D LEU* 3.9 22.7 - - + -
3137D MET* 4.0 21.8 - - + -
3138D PHE 4.4 1.8 - - - +
3139D ALA* 5.3 0.2 - - + -
3167D TRP* 3.8 30.3 - - + -
3431D TYR* 4.3 7.6 - - + -
3432D VAL 3.8 5.4 - - - +
3434D LEU* 4.4 4.3 - - - -
3449D ASN* 3.8 3.4 - - - +
3450D SER* 1.3 82.7 + - - +
3452D VAL* 1.3 74.7 + - - +
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Residues in contact with VAL3452 (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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3105D ILE* 3.6 21.3 - - + -
3107D SER 3.5 12.1 - - - +
3108D LYS* 4.2 9.4 - - + -
3403D ILE* 4.6 4.3 - - + -
3404D VAL* 4.9 0.4 - - + -
3431D TYR* 3.2 5.0 - - - +
3432D VAL* 2.9 56.6 + - + +
3434D LEU* 4.4 6.7 - - + -
3451D ILE* 1.3 78.1 - - - +
3453D ALA* 1.3 63.1 + - - +
3454D LEU* 4.1 11.2 - - + +
3466D TRP* 3.6 37.5 - - + +
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Residues in contact with ALA3453 (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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3105D ILE* 3.5 1.7 - - - +
3106D LEU* 2.9 31.4 + - + -
3107D SER* 2.8 23.8 + - - +
3128D LEU* 4.1 20.2 - - + -
3137D MET* 5.6 0.2 - - + -
3416D PHE* 4.1 18.8 - - + -
3430D PHE 3.3 12.1 - - - +
3451D ILE* 5.1 0.7 - - + -
3452D VAL* 1.3 76.4 - - - +
3454D LEU* 1.3 68.2 + - - +
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Residues in contact with LEU3454 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3103D TRP* 4.1 23.8 - - + +
3104D HIS 3.2 22.9 - - - +
3105D ILE* 4.2 5.8 - - + +
3106D LEU* 3.9 2.0 - - - +
3401D GLN* 4.3 3.4 - - - +
3403D ILE* 3.6 38.1 - - + -
3429D CYS* 3.2 3.5 - - - +
3430D PHE* 2.9 54.6 + - + +
3452D VAL* 4.1 16.6 - - + -
3453D ALA* 1.3 82.6 - - - +
3455D CYS* 1.3 62.7 + - - +
3466D TRP* 4.3 20.0 - - + +
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Residues in contact with CYS3455 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2218C PRO* 5.3 3.6 - - + -
3103D TRP* 3.3 8.8 - - - -
3104D HIS* 2.8 49.6 + - - +
3106D LEU* 3.8 29.6 - - - -
3427D ASN* 3.9 7.2 - - - +
3428D PRO 3.3 5.6 - - - +
3429D CYS* 2.0 46.9 - - - -
3454D LEU* 1.3 73.7 - - - +
3456D GLY* 1.3 63.5 + - - +
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Residues in contact with GLY3456 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2221C GLU* 4.7 2.6 - - - +
3100D VAL* 3.8 10.8 - - - -
3102D SER 3.6 7.4 - - - -
3103D TRP* 3.3 9.5 - - - -
3104D HIS* 3.6 9.4 - - - -
3427D ASN* 2.8 36.2 + - - +
3428D PRO 2.8 14.0 + - - -
3455D CYS* 1.3 77.1 - - - +
3457D SER* 1.3 59.0 + - - -
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Residues in contact with SER3457 (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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2221C GLU* 2.9 30.7 + - - -
3099D GLU 4.3 3.8 - - - -
3100D VAL* 4.1 0.6 - - - +
3101D ASN 2.8 23.4 + - - -
3102D SER* 2.8 20.1 + - - -
3104D HIS* 4.6 2.7 - - - -
3427D ASN* 5.3 0.2 - - - +
3456D GLY* 1.3 74.3 - - - -
3458D LYS* 1.3 59.3 + - - +
3459D LYS* 3.0 23.1 + - - +
3461D LEU* 3.9 20.8 - - - +
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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