Contacts of the strand formed by residues 439 - 449 (chain N) in PDB entry 1A14
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 439 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116N VAL* 3.3 19.4 - - - +
117N THR 4.5 0.7 - - - +
118N ARG* 4.1 16.1 - - - +
148N THR* 3.1 20.9 + - - +
149N ILE* 3.4 17.9 - - + +
427N ILE* 3.3 23.6 - - + -
428N ARG 3.3 4.5 - - - +
430N ARG* 2.9 41.2 + - - +
431N PRO* 5.2 0.7 - - + -
438N TRP* 1.3 73.7 - - - +
440N SER* 1.3 69.6 + - - +
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Residues in contact with SER 440 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106N VAL* 4.6 8.2 - - - +
115N LEU 4.1 3.3 + - - -
116N VAL* 3.4 12.9 - - - +
117N THR* 3.2 30.6 + - - -
118N ARG* 4.4 0.9 - - - -
140N ILE* 4.8 9.0 - - - +
427N ILE* 3.0 9.0 - - - +
428N ARG 2.8 29.1 + - - -
438N TRP* 3.8 17.5 - - - -
439N THR* 1.3 78.6 - - - +
441N ASN* 1.3 68.3 + - - +
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Residues in contact with ASN 441 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N ASP* 5.0 0.7 + - - +
105N ALA* 4.2 9.5 - - - +
106N VAL* 3.7 16.3 - - - +
117N THR* 2.8 45.6 + - - +
118N ARG* 3.2 7.6 - - + -
120N PRO* 3.4 27.7 - - - +
167N PRO* 6.1 0.3 - - - +
425N GLU* 3.6 24.0 - - + +
426N LEU 3.0 14.6 - - - +
427N ILE* 4.2 1.1 - - - -
440N SER* 1.3 82.1 + - - +
442N SER* 1.3 75.2 + - - +
443N ILE* 3.9 3.6 - - - +
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Residues in contact with SER 442 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N LYS* 4.7 2.4 + - - -
103N ASP* 2.9 17.6 + - - -
104N ASN* 3.6 13.2 + - - -
105N ALA* 4.5 5.2 - - - -
106N VAL 4.7 0.9 - - - -
424N VAL 3.6 1.6 - - - +
425N GLU* 3.7 0.2 - - - -
426N LEU* 2.8 35.6 + - - +
441N ASN* 1.3 82.5 + - - +
443N ILE* 1.3 67.0 + - - +
460N ASP* 3.0 37.9 + - - -
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Residues in contact with ILE 443 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N LYS* 3.4 8.1 - - - +
103N ASP* 2.9 35.2 + - - +
120N PRO* 3.8 32.1 - - + -
121N TYR 5.0 1.8 - - - +
122N VAL* 4.8 0.9 - - + -
131N PHE* 3.6 55.6 - - + -
132N TYR 4.8 1.3 - - - +
161N TRP* 3.9 16.6 - - + -
423N TYR* 4.0 24.9 - - + -
424N VAL 3.6 3.8 - - - +
426N LEU* 4.9 1.6 - - - -
441N ASN* 3.9 2.7 - - - +
442N SER* 1.3 82.3 + - - +
444N VAL* 1.3 67.1 + - - +
445N SER 4.3 0.2 - - - +
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Residues in contact with VAL 444 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N ILE* 4.5 9.2 - - + -
101N GLY 3.5 8.3 - - - +
102N LYS* 4.3 12.3 - - + -
397N ILE* 4.6 10.1 - - + -
422N PHE* 5.2 0.3 - - - -
423N TYR* 3.1 1.0 - - - -
424N VAL* 2.8 51.3 + - + +
426N LEU* 3.9 22.7 - - + -
443N ILE* 1.3 75.5 - - - +
445N SER* 1.3 62.9 + - - +
446N MET* 4.3 5.5 - - + +
458N TRP* 3.4 39.0 - - + +
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Residues in contact with SER 445 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N ILE* 4.1 2.3 - - - +
100N TYR* 2.9 55.5 + - - +
101N GLY* 2.8 22.7 + - - +
122N VAL* 3.8 23.6 - - - -
131N PHE* 4.3 5.4 - - - -
410N PHE* 4.5 0.4 - - - -
422N PHE 2.9 17.3 - - - -
423N TYR* 3.8 1.3 - - - -
443N ILE* 4.3 3.8 - - - -
444N VAL* 1.3 74.3 - - - +
446N MET* 1.3 56.8 + - - +
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Residues in contact with MET 446 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97N TRP* 3.3 32.3 - - + +
98N HIS 3.4 23.6 - - - +
99N ILE* 4.1 15.0 - - + -
100N TYR* 4.2 0.4 - - - -
395N GLN* 3.6 17.0 - - - +
396N THR 5.4 0.9 - - - +
397N ILE* 3.8 30.5 - - + -
421N CYS* 3.1 5.0 - - - +
422N PHE* 2.7 69.1 + - + +
444N VAL* 4.4 5.1 + - + +
445N SER* 1.3 77.4 - - - +
447N CYS* 1.3 62.3 + - - +
456N TRP 5.9 0.9 - - - +
458N TRP* 4.4 15.5 - - + +
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Residues in contact with CYS 447 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97N TRP* 3.6 6.1 - - - -
98N HIS* 2.7 65.9 + - + +
100N TYR* 3.6 31.4 - - + +
419N ARG* 4.4 7.9 - - - -
420N ALA 3.5 4.9 - - - +
421N CYS* 2.0 46.0 - - - +
446N MET* 1.3 73.0 - - - +
448N SER* 1.3 56.0 + - - +
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Residues in contact with SER 448 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92N CYS* 5.2 3.9 - - - +
93N THR 4.9 2.2 - - - -
94N ILE* 4.0 34.1 - - - +
96N SER 3.5 7.4 - - - -
97N TRP* 3.4 8.0 - - - -
98N HIS* 3.7 1.3 - - - -
419N ARG* 3.4 35.9 + - - +
420N ALA 3.0 31.3 + - - -
447N CYS* 1.3 74.3 - - - +
449N SER* 1.3 62.2 + - - +
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Residues in contact with SER 449 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N THR 3.7 2.9 - - - +
94N ILE 3.9 0.2 - - - -
95N ASN 2.8 24.4 + - - -
96N SER* 3.2 27.5 + - - -
97N TRP 4.5 0.2 - - - -
98N HIS* 4.3 8.3 - - - -
419N ARG* 5.3 4.0 - - - +
447N CYS 3.7 0.4 + - - -
448N SER* 1.3 75.3 - - - +
450N THR* 1.3 60.4 + - - +
451N GLU* 2.8 32.1 + - - +
453N LEU* 3.5 18.7 - - - +
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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