Contacts of the strand formed by residues 3379 - 3385 (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 SER3379 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3372D THR* 3.7 1.2 - - - -
3373D ILE 3.2 13.0 + - - -
3374D SER* 3.2 17.2 + - - -
3377D SER* 2.8 9.4 + - - -
3378D ARG* 1.3 74.6 - - - +
3380D GLY* 1.3 67.0 + - - +
3406D ASN* 2.8 27.8 + - - -
3408D ASN 3.4 3.8 - - - -
3409D TRP* 3.7 7.4 - - - -
3410D SER* 3.4 1.5 + - - -
4478D SIA 3.3 43.6 + - - -
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Residues in contact with GLY3380 (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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3372D THR* 3.4 6.9 - - - -
3373D ILE* 3.7 7.2 - - - -
3379D SER* 1.3 75.9 - - - +
3381D TYR* 1.3 60.8 + - - +
3404D VAL* 3.1 16.4 - - - -
3405D ASN 3.2 15.6 + - - -
3406D ASN* 3.7 5.6 - - - +
3408D ASN 2.8 15.3 + - - -
3410D SER* 2.7 23.9 + - - +
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Residues in contact with TYR3381 (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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3358D GLY* 4.9 0.3 - - - -
3359D PHE* 3.3 17.5 + + - -
3370D GLY* 3.3 18.1 + - - -
3371D ARG* 3.5 34.0 - - - -
3372D THR* 4.0 7.6 - - + -
3373D ILE* 3.5 3.8 - - - +
3380D GLY* 1.3 77.9 - - - +
3382D GLU* 1.3 76.1 + - - +
3383D MET* 4.0 10.1 - - - -
3402D VAL* 3.8 1.7 - - - +
3403D ILE* 2.8 32.4 + - + -
3404D VAL* 2.7 33.9 + - + +
3410D SER* 4.3 8.3 - - - -
3411D GLY 4.8 4.0 - - - -
3413D SER* 2.6 39.0 + - - -
3430D PHE* 4.4 0.7 - + - -
3432D VAL* 3.9 27.4 - - + -
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Residues in contact with GLU3382 (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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3369D LEU 3.9 0.5 - - - +
3370D GLY* 3.4 3.6 - - - -
3371D ARG* 2.8 79.9 + - + +
3372D THR 4.0 5.0 - - - +
3373D ILE* 3.9 30.8 - - + +
3381D TYR* 1.3 76.8 - - - +
3383D MET* 1.3 63.1 + - - +
3384D LEU* 3.6 24.2 - - + +
3400D ASN* 5.2 4.1 - - + +
3401D GLN 3.6 10.1 - - - +
3402D VAL* 4.7 6.8 - - + +
3403D ILE 4.4 0.4 - - - +
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Residues in contact with MET3383 (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 44.9 - - + +
3359D PHE* 3.5 37.7 - - + -
3368D TRP* 3.9 20.8 - - + -
3369D LEU 3.5 0.7 - - - -
3370D GLY* 3.5 20.2 - - - +
3381D TYR* 4.0 5.6 - - - -
3382D GLU* 1.3 72.0 - - - +
3384D LEU* 1.3 63.4 + - - +
3400D ASN* 3.1 5.7 - - - -
3401D GLN* 3.0 36.3 + - + +
3403D ILE* 3.8 12.8 - - + -
3430D PHE* 3.7 26.9 - - + -
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Residues in contact with LEU3384 (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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3490C BMA 5.6 0.7 - - - +
3328D VAL* 3.7 15.9 - - + -
3368D TRP* 3.4 4.2 - - - -
3369D LEU* 2.8 43.9 + - + +
3371D ARG* 3.3 44.4 - - + +
3382D GLU* 3.6 25.4 - - + +
3383D MET* 1.3 75.1 - - - +
3385D LYS* 1.3 61.7 + - - +
3386D VAL* 3.4 13.6 + - + +
3397D PRO* 4.3 17.7 - - + -
3399D SER 3.4 4.9 - - - +
3400D ASN* 3.6 23.3 - - + -
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Residues in contact with LYS3385 (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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3099D GLU* 5.3 2.4 - - - +
3100D VAL 2.9 14.8 + - - +
3101D ASN* 2.9 28.6 + - - +
3365D GLU 3.7 20.9 - - - +
3366D ASN* 4.5 9.3 + - - +
3367D SER 3.4 14.4 - - - +
3368D TRP* 3.4 31.7 - - + +
3384D LEU* 1.3 71.4 - - - +
3386D VAL* 1.3 59.1 + - - +
3387D PRO* 3.8 0.2 - - - -
3397D PRO* 3.3 2.3 - - - +
3398D ILE* 2.8 52.1 + - + +
3399D SER* 3.0 30.3 + - - +
3460D ARG* 5.8 1.5 - - - +
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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