Contacts of the strand formed by residues 3102 - 3108 (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 SER3102 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3100D VAL* 3.3 10.2 - - - +
3101D ASN* 1.3 76.3 - - - +
3103D TRP* 1.3 70.2 + - - +
3368D TRP* 4.4 2.2 - - - -
3401D GLN* 3.6 13.2 - - - -
3456D GLY* 3.6 0.2 - - - -
3457D SER* 2.8 25.4 + - - -
3459D LYS 2.8 20.0 + - - -
3460D ARG* 4.3 2.0 - - - -
3461D LEU* 3.0 38.9 + - - +
2H NAG 4.4 7.2 - - - -
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Residues in contact with TRP3103 (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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3100D VAL* 3.8 12.3 - - + -
3102D SER* 1.3 78.8 + - - +
3104D HIS* 1.3 60.3 + - - +
3105D ILE 4.3 0.3 + - - -
3361D PHE* 4.2 13.0 - + - -
3368D TRP* 3.3 52.7 - + + -
3383D MET* 3.7 31.5 - - + +
3401D GLN* 2.8 43.7 + - - +
3403D ILE* 4.8 0.7 - - + -
3428D PRO* 3.5 42.0 - - + -
3429D CYS* 4.5 0.2 - - - -
3430D PHE* 3.7 26.2 - + + -
3454D LEU* 4.1 16.8 - - + +
3455D CYS* 3.3 9.0 - - - +
3456D GLY* 3.3 21.3 - - - -
3461D LEU* 4.2 10.9 - - - +
3462D GLY 5.0 2.8 - - - +
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Residues in contact with HIS3104 (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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2209C SER* 5.8 0.9 - - - +
2211C VAL* 3.8 14.4 - - + +
2213C TRP* 5.3 0.2 - + - -
2218C PRO* 3.8 33.1 - - + +
2221C GLU* 3.8 26.4 + - + -
3102D SER 4.4 0.2 - - - -
3103D TRP* 1.3 73.8 - - - +
3105D ILE* 1.3 88.0 + - - +
3106D LEU* 4.2 5.6 - - + -
3427D ASN* 4.8 2.0 + - - -
3454D LEU* 3.2 6.4 - - - +
3455D CYS* 2.8 66.9 + - + +
3456D GLY 3.6 15.1 + - - -
3457D SER* 4.6 0.8 - - - -
3461D LEU* 3.5 24.8 - - + +
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Residues in contact with ILE3105 (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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2183C ILE* 3.6 43.4 + - + +
2202C SER* 3.6 22.9 - - - +
2209C SER* 6.1 0.4 - - - +
2211C VAL* 4.0 17.5 - - + +
2213C TRP* 4.5 5.5 + - - -
3103D TRP 4.3 0.4 + - - -
3104D HIS* 1.3 87.7 + - - +
3106D LEU* 1.3 59.8 + - - +
3107D SER 3.7 6.7 - - - +
3108D LYS* 4.9 0.2 - - + -
3452D VAL* 3.6 25.4 - - + -
3453D ALA 3.5 18.2 - - - +
3454D LEU* 4.2 8.3 - - + +
3466D TRP* 3.6 31.6 - - + +
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Residues in contact with LEU3106 (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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2180C VAL* 6.0 0.5 - - - +
2182C CYS* 5.4 0.3 - - - -
2183C ILE* 3.7 8.8 - - - +
2213C TRP* 3.3 47.6 - - + -
2218C PRO* 3.7 25.1 - - + -
3104D HIS* 3.4 3.9 + - + -
3105D ILE* 1.3 75.4 - - - +
3107D SER* 1.3 59.6 + - - +
3135D CYS* 5.5 4.3 - - - -
3169D MET* 3.8 26.2 - - + +
3416D PHE* 3.6 33.9 - - + -
3453D ALA* 2.9 24.3 + - + +
3454D LEU* 4.1 5.6 - - - -
3455D CYS* 3.8 20.2 - - - -
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Residues in contact with SER3107 (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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2180C VAL* 5.2 2.0 - - - +
2183C ILE* 3.6 14.0 - - - +
3105D ILE* 3.7 1.8 - - - +
3106D LEU* 1.3 81.6 - - - +
3108D LYS* 1.3 61.2 + - - +
3137D MET* 3.3 10.0 - - - +
3169D MET* 3.3 24.4 - - - +
3170D GLY* 3.2 32.2 + - - -
3452D VAL* 3.5 5.2 - - - +
3453D ALA* 2.8 34.2 + - - +
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Residues in contact with LYS3108 (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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2160C PRO 3.2 26.7 - - - +
2161C PHE* 3.9 3.0 - - - -
2180C VAL* 5.4 1.2 - - - +
2183C ILE* 3.6 23.1 - - + +
3105D ILE* 4.9 0.7 - - + -
3107D SER* 1.3 78.3 + - - +
3109D ASP* 1.3 62.8 + - - +
3110D ASN* 2.7 40.1 + - - +
3137D MET* 4.8 0.9 - - - -
3170D GLY* 3.7 10.2 - - - +
3434D LEU* 4.6 3.7 - - - +
3450D SER* 4.6 1.0 + - - -
3451D ILE 3.2 16.4 - - - +
3452D VAL* 4.2 7.9 - - + -
3466D TRP* 3.5 30.3 - - + +
3467D HIS 3.1 18.3 + - - -
3468D ASP* 3.1 24.4 + - - +
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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