Contacts of the strand formed by residues 3428 - 3437 (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 PRO3428 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3097D LEU* 3.7 24.7 - - + -
3098D CYS 4.1 5.6 - - - +
3100D VAL* 3.9 17.5 - - + -
3103D TRP* 3.5 13.9 - - + -
3361D PHE* 3.6 39.9 - - + -
3366D ASN* 5.6 0.7 - - - +
3368D TRP* 6.5 0.2 - - + -
3417D ILE* 4.1 3.1 - - + -
3426D PHE 3.4 9.8 - - - +
3427D ASN* 1.4 93.9 - - - +
3429D CYS* 1.3 56.0 + - - +
3455D CYS* 3.3 2.8 - - - +
3456D GLY 2.8 31.4 + - - -
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Residues in contact with CYS3429 (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* 4.5 0.9 - - - -
3106D LEU* 4.8 0.2 - - - -
3361D PHE* 3.2 13.5 - - - -
3416D PHE* 2.9 62.5 + - + +
3417D ILE* 4.8 3.8 - - - -
3418D ASP* 4.8 7.6 - - - -
3427D ASN* 3.9 9.9 - - - -
3428D PRO* 1.3 74.1 - - - +
3430D PHE* 1.3 61.7 + - - +
3454D LEU 3.2 5.8 - - - +
3455D CYS* 2.0 47.3 - - - +
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Residues in contact with PHE3430 (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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3103D TRP* 3.7 38.6 - + - -
3359D PHE* 3.3 34.3 - + + -
3381D TYR* 4.4 2.0 - + - -
3383D MET* 3.7 27.1 - - + -
3403D ILE* 3.9 18.8 - - + -
3414D GLY 3.1 15.3 - - - +
3416D PHE* 3.6 6.7 - - - -
3429D CYS* 1.3 75.2 - - - +
3431D TYR* 1.3 71.6 + - - +
3432D VAL* 3.7 21.8 - - + -
3453D ALA* 3.3 4.3 - - - +
3454D LEU* 2.9 59.3 + - + +
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Residues in contact with TYR3431 (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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3126D PRO* 3.0 34.5 + - + -
3127D TYR* 3.4 24.7 - - + -
3128D LEU* 3.6 27.6 - - + -
3234D GLU 3.4 4.5 + - - -
3235D SER* 3.4 4.3 - - - -
3357D LYS* 3.1 32.4 - - - +
3412D TYR* 4.2 8.0 - - + +
3413D SER* 3.3 27.2 - - - -
3414D GLY* 3.1 37.1 + - - -
3415D ALA 4.9 2.0 - - - -
3416D PHE* 4.4 5.8 - + - -
3430D PHE* 1.3 78.1 - - - +
3432D VAL* 1.3 72.3 + - - +
3433D GLU 4.0 5.4 - - - -
3451D ILE* 4.3 3.1 - - + -
3452D VAL 3.2 13.2 - - - +
3453D ALA* 4.3 0.4 - - + -
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Residues in contact with VAL3432 (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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3381D TYR* 3.9 31.6 - - + -
3403D ILE* 4.3 11.7 - - + -
3404D VAL* 4.5 0.7 - - + -
3410D SER* 4.0 21.5 - - - -
3412D TYR 3.6 7.4 - - - +
3413D SER* 4.6 0.4 - - - -
3430D PHE* 3.7 22.7 - - + -
3431D TYR* 1.3 82.6 - - - +
3433D GLU* 1.3 73.4 + - - +
3434D LEU* 3.6 12.6 + - + +
3451D ILE* 3.8 3.0 - - - -
3452D VAL* 2.9 39.7 + - + +
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Residues in contact with GLU3433 (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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3124D ARG* 2.7 51.8 + - - +
3125D GLU 2.8 17.0 + - - -
3126D PRO* 3.3 31.5 - - + +
3410D SER* 2.9 3.5 - - - -
3411D GLY 2.9 27.9 + - - -
3412D TYR* 2.6 38.9 + - + +
3431D TYR* 4.0 2.6 - - + -
3432D VAL* 1.3 72.3 - - - +
3434D LEU* 1.3 61.0 + - - +
3435D ILE* 3.4 10.0 - - + +
3449D ASN* 3.7 11.0 - - + -
3450D SER 3.9 4.0 - - - -
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Residues in contact with LEU3434 (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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3108D LYS* 4.6 3.4 - - - +
3404D VAL* 3.8 29.8 - - + -
3409D TRP 3.8 19.5 - - - +
3410D SER* 4.5 0.4 - - - -
3432D VAL* 3.8 22.4 - - + +
3433D GLU* 1.3 73.4 - - - +
3435D ILE* 1.3 63.1 + - - +
3436D ARG* 3.5 7.5 + - - +
3449D ASN* 3.2 4.2 - - - -
3450D SER* 3.0 51.2 + - - +
3451D ILE 4.4 7.2 - - - -
3452D VAL* 4.4 10.1 - - + -
3466D TRP 3.5 14.4 - - - +
3467D HIS 3.9 0.2 - - - -
3468D ASP* 3.5 28.0 - - + +
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Residues in contact with ILE3435 (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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3124D ARG* 3.7 21.3 - - - +
3378D ARG* 4.2 17.3 - - + +
3409D TRP* 3.2 26.9 + - + +
3410D SER 3.1 13.8 + - - +
3411D GLY* 3.6 14.6 - - - -
3433D GLU* 3.4 34.3 - - - +
3434D LEU* 1.3 69.6 - - - +
3436D ARG* 1.3 70.6 + - - +
3437D GLY 5.3 1.3 - - - +
3438D ARG 4.4 7.9 - - - +
3439D PRO* 5.9 1.3 - - + -
3447D THR* 4.3 15.5 - - + -
3448D SER 3.3 12.8 - - - +
3449D ASN* 4.1 0.7 - - - -
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Residues in contact with ARG3436 (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 16.8 - - + -
3408D ASN* 5.6 3.6 + - - -
3409D TRP* 4.2 12.1 - - - +
3434D LEU 3.5 3.8 + - - +
3435D ILE* 1.3 86.7 - - - +
3437D GLY* 1.3 62.9 + - - +
3441D GLU* 2.8 40.3 + - - +
3446D TRP* 3.6 20.3 - - + -
3447D THR* 3.6 1.2 - - - -
3448D SER 2.8 31.1 + - - +
3468D ASP* 2.8 60.5 + - - +
3469D GLY 4.4 1.4 - - - +
3470D ALA* 3.0 31.8 + - - +
3472D ILE* 3.8 22.0 - - + +
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Residues in contact with GLY3437 (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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3435D ILE* 5.3 1.6 - - - +
3436D ARG* 1.3 74.1 - - - +
3438D ARG* 1.3 65.1 + - - +
3440D LYS* 3.4 4.5 + - - +
3441D GLU* 2.8 51.4 + - - +
3444D VAL* 3.6 11.0 - - - -
3446D TRP* 3.4 14.3 - - - -
3472D ILE* 4.5 1.2 - - - +
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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