Contacts of the strand formed by residues 102 - 108 (chain A) 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 SER 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A VAL* 3.4 8.5 - - - +
101A ASN* 1.3 78.7 - - - +
103A TRP* 1.3 70.3 + - - +
368A TRP* 4.6 0.4 - - - -
401A GLN* 3.7 11.4 - - - -
456A GLY* 3.6 0.2 - - - -
457A SER* 2.8 27.6 + - - +
459A LYS 2.6 23.5 + - - -
460A ARG* 4.3 1.6 - - - -
461A LEU* 3.1 36.6 + - - +
2E NAG 4.1 7.6 - - - -
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Residues in contact with TRP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 3.7 13.2 - - + -
102A SER* 1.3 78.6 - - - +
104A HIS* 1.3 61.5 + - - +
361A PHE* 4.2 12.3 - + - -
368A TRP* 3.2 54.4 - + + -
383A MET* 3.6 31.3 - - + +
401A GLN* 2.9 43.6 + - - +
403A ILE* 4.7 0.9 - - + -
428A PRO* 3.5 41.3 - - + -
430A PHE* 3.5 29.4 - + + -
454A LEU* 4.0 16.8 - - + +
455A CYS* 3.4 22.9 - - - +
456A GLY* 3.4 4.9 - - - -
461A LEU* 4.4 10.5 - - - +
462A GLY 5.0 2.9 - - - +
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Residues in contact with HIS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER 4.3 0.2 - - - -
103A TRP* 1.3 73.7 - - - +
105A ILE* 1.3 87.0 + - - +
106A LEU* 4.4 5.6 - - + -
427A ASN* 4.8 1.6 + - - -
454A LEU* 3.1 8.3 - - - +
455A CYS* 2.9 65.8 + - + +
456A GLY 3.5 15.8 + - - -
457A SER* 4.6 0.6 - - - -
461A LEU* 3.5 25.3 - - + +
1209B SER* 5.8 1.1 - - - +
1211B VAL* 3.7 18.6 - - + +
1213B TRP* 5.2 0.2 - + - -
1218B PRO* 3.7 32.4 - - + +
1221B GLU* 4.0 24.3 + - + -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A HIS* 1.3 85.6 + - - +
106A LEU* 1.3 59.5 + - - +
107A SER 3.8 8.3 - - - +
108A LYS* 4.8 0.7 - - + -
452A VAL* 3.7 24.9 - - + -
453A ALA 3.5 16.4 - - - +
454A LEU* 4.1 7.0 - - + +
466A TRP* 3.5 41.1 - - + +
1183B ILE* 3.7 34.2 + - + +
1202B SER* 3.6 22.0 - - - +
1209B SER* 5.9 1.3 - - - +
1211B VAL* 4.1 15.7 - - + +
1213B TRP* 4.5 5.5 + - - -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A HIS* 3.4 3.0 + - + -
105A ILE* 1.3 75.6 - - - +
107A SER* 1.3 60.9 + - - +
135A CYS* 5.4 4.7 - - - -
169A MET* 3.8 25.9 - - + +
416A PHE* 3.6 34.5 - - + -
453A ALA* 2.8 26.3 + - + +
454A LEU* 4.1 5.2 - - - -
455A CYS* 3.7 19.7 - - - +
1182B CYS* 5.3 0.5 - - - -
1183B ILE* 3.9 9.7 - - - +
1213B TRP* 3.3 46.7 - - + -
1218B PRO* 3.7 26.0 - - + -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 3.8 2.0 - - - +
106A LEU* 1.3 84.8 - - - +
108A LYS* 1.3 68.4 + - - +
137A MET* 3.5 10.1 - - - +
169A MET* 3.3 24.9 - - - +
170A GLY* 3.2 31.4 + - - -
452A VAL* 3.4 3.3 - - - +
453A ALA* 2.7 33.9 + - - +
1180B VAL* 5.3 1.0 - - - +
1183B ILE* 3.7 12.7 - - - +
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 4.8 0.9 - - + -
107A SER* 1.3 80.4 + - - +
109A ASP* 1.4 62.1 + - - +
110A ASN* 2.8 39.2 + - - +
137A MET* 4.6 1.1 - - - -
170A GLY* 3.6 10.1 - - - +
434A LEU* 4.6 4.3 - - - +
450A SER* 4.7 1.4 + - - -
451A ILE 3.3 17.7 - - - +
452A VAL* 4.2 7.9 - - + -
466A TRP* 3.4 30.3 - - + +
467A HIS 3.0 29.3 + - - -
468A ASP* 3.3 12.1 + - - +
1160B PRO 3.3 25.1 - - - +
1161B PHE* 3.9 3.7 - - - -
1180B VAL* 5.4 1.0 - - - +
1183B ILE* 3.7 25.2 - - + +
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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