Contacts of the strand formed by residues 447 - 457 (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 THR 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A VAL* 3.2 21.4 - - - +
123A THR 3.9 2.3 - - - +
124A ARG* 3.8 27.7 - - - +
142A GLN* 5.3 0.5 + - - +
154A THR* 3.2 25.1 + - - +
155A ILE* 3.4 18.6 - - + +
435A ILE* 4.0 12.1 - - + -
436A ARG 3.5 5.4 - - - -
438A ARG* 2.9 39.9 + - - +
446A TRP* 1.3 72.5 - - - +
448A SER* 1.3 63.9 + - - +
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Residues in contact with SER 448 (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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112A ILE* 3.8 17.1 - - - +
121A LEU 4.3 2.8 + - - -
122A VAL* 3.7 9.0 - - - -
123A THR* 3.2 29.9 + - - -
124A ARG* 4.4 1.7 - - - +
146A LEU* 3.9 19.2 - - - +
435A ILE* 3.5 8.8 - - - +
436A ARG 3.0 27.2 + - - +
446A TRP* 3.6 2.1 - - - -
447A THR* 1.3 78.4 - - - +
449A ASN* 1.4 74.7 + - - +
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Residues in contact with ASN 449 (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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111A ALA* 4.0 8.5 - - - +
112A ILE* 3.4 17.9 - - - +
123A THR* 2.8 34.7 + - - -
124A ARG* 2.9 29.0 - - + +
126A PRO* 3.6 16.7 - - - +
173A PRO* 6.1 0.3 - - - +
433A GLU* 3.6 26.2 - - + +
434A LEU 3.1 16.6 - - - +
435A ILE* 4.1 1.1 - - - -
448A SER* 1.4 83.5 + - - +
450A SER* 1.3 78.8 + - - +
451A ILE* 3.8 4.5 - - - +
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Residues in contact with SER 450 (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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108A LYS* 4.7 2.1 + - - -
109A ASP* 3.6 11.7 - - - -
110A ASN 4.4 3.4 - - - -
111A ALA* 3.6 20.2 - - - -
112A ILE* 4.0 1.8 - - - +
433A GLU* 3.9 1.0 - - - -
434A LEU* 3.0 43.7 + - - +
449A ASN* 1.3 83.8 - - - +
451A ILE* 1.3 68.3 + - - +
468A ASP* 2.6 30.5 + - - +
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Residues in contact with ILE 451 (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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108A LYS* 3.3 9.1 - - - +
109A ASP* 2.8 44.0 + - - +
110A ASN 4.5 0.3 + - - -
126A PRO* 3.7 31.2 - - + -
128A LEU* 4.0 22.9 - - + -
137A MET* 4.0 22.2 - - + -
138A PHE 4.5 1.6 - - - +
167A TRP* 3.8 30.5 - - + -
431A TYR* 4.3 6.7 - - + -
432A VAL 3.8 7.6 - - - +
434A LEU* 4.4 4.0 - - - -
449A ASN* 3.8 3.8 - - - +
450A SER* 1.3 80.5 + - - +
452A VAL* 1.3 74.2 + - - +
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Residues in contact with VAL 452 (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* 3.7 20.6 - - + -
107A SER 3.4 5.8 - - - +
108A LYS* 4.2 8.3 - - + -
403A ILE* 4.7 3.6 - - + -
404A VAL* 4.9 0.7 - - + -
431A TYR* 3.2 6.2 - - - +
432A VAL* 3.1 55.7 + - + +
434A LEU* 4.1 13.5 - - + -
451A ILE* 1.3 77.0 - - - +
453A ALA* 1.3 62.0 + - - +
454A LEU* 4.1 10.7 - - + +
466A TRP* 3.5 37.7 - - + +
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Residues in contact with ALA 453 (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* 3.5 2.1 - - - +
106A LEU* 2.8 37.3 + - + -
107A SER* 2.7 20.0 + - - +
128A LEU* 4.2 18.6 - - + -
137A MET* 5.4 0.2 - - + -
416A PHE* 4.1 19.7 - - + -
430A PHE 3.2 13.2 - - - +
431A TYR* 4.4 2.0 - - + -
451A ILE* 5.1 0.7 - - + -
452A VAL* 1.3 74.6 - - - +
454A LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 454 (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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103A TRP* 4.0 28.7 - - + +
104A HIS 3.1 22.0 - - - +
105A ILE* 4.1 6.1 - - + +
106A LEU 3.9 2.0 - - - +
401A GLN* 4.2 8.3 - - - +
403A ILE* 3.7 30.5 - - + -
429A CYS* 3.2 4.2 - - - +
430A PHE* 2.9 54.5 + - + -
452A VAL* 4.1 16.6 - - + -
453A ALA* 1.3 83.3 - - - +
455A CYS* 1.3 62.2 + - - +
466A TRP* 4.1 20.2 - - + +
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Residues in contact with CYS 455 (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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103A TRP* 3.4 8.5 - - - -
104A HIS* 2.9 49.2 + - - +
106A LEU* 3.7 30.7 - - - +
427A ASN* 3.9 7.9 - - - +
428A PRO 3.2 5.6 - - - +
429A CYS* 2.0 46.7 - - - -
454A LEU* 1.3 73.5 - - - +
456A GLY* 1.3 63.3 + - - +
1218B PRO* 5.4 2.9 - - + -
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Residues in contact with GLY 456 (chain A).
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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100A VAL* 3.7 10.8 - - - -
102A SER 3.6 7.6 - - - -
103A TRP* 3.4 10.6 - - - -
104A HIS* 3.5 9.7 - - - -
423A LYS* 5.2 0.9 + - - -
427A ASN* 2.7 35.6 + - - +
428A PRO 2.8 14.9 + - - -
455A CYS* 1.3 75.8 - - - +
457A SER* 1.3 59.9 - - - -
1221B GLU* 4.7 2.8 - - - +
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Residues in contact with SER 457 (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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99A GLU 4.2 4.7 - - - -
100A VAL* 4.1 0.6 - - - +
101A ASN 2.7 30.6 + - - -
102A SER* 2.8 22.9 + - - -
104A HIS* 4.6 3.1 - - - -
456A GLY* 1.3 75.3 - - - -
458A LYS* 1.3 53.1 + - - +
459A LYS* 3.1 21.4 + - - +
461A LEU* 3.7 23.1 - - - +
1221B GLU* 2.6 29.6 + - - -
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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