Contacts of the strand formed by residues 96 - 102 (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 SER 96 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94N ILE* 3.8 3.5 - - - +
95N ASN* 1.3 77.6 - - - +
97N TRP* 1.3 82.0 + - - +
361N TRP* 4.8 2.9 - - - -
392N GLN* 5.0 1.3 - - - +
395N GLN* 4.0 13.2 - - - -
448N SER* 3.5 5.4 - - - -
449N SER* 3.2 21.7 + - - +
451N GLU 2.8 20.4 + - - -
452N PHE* 4.0 1.3 - - - -
453N LEU* 3.0 38.6 + - - +
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Residues in contact with TRP 97 (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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94N ILE* 3.6 26.2 - - + -
96N SER* 1.3 83.9 + - - +
98N HIS* 1.3 61.2 + - - +
354N TYR* 4.1 20.4 - + - -
361N TRP* 3.2 38.6 - + + -
376N MET* 3.4 35.1 - - + +
395N GLN* 3.2 35.5 + - + +
420N ALA* 3.9 15.0 - - + -
422N PHE* 3.5 25.4 - + - -
446N MET* 3.3 24.9 - - + +
447N CYS* 3.3 11.2 - - - +
448N SER* 3.4 28.9 - - - +
449N SER 4.3 0.4 - - - +
453N LEU* 4.4 6.9 - - - +
454N GLY 5.4 1.6 - - - +
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Residues in contact with HIS 98 (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* 1.3 75.8 - - - +
99N ILE* 1.3 87.2 + - + +
100N TYR* 5.1 5.8 - + + -
419N ARG* 3.4 32.8 + - - -
446N MET* 3.4 8.0 - - - +
447N CYS* 2.7 68.6 + - + +
448N SER 3.7 11.0 - - - -
449N SER* 4.3 6.7 - - - -
453N LEU* 3.6 21.5 - - + -
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Residues in contact with ILE 99 (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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98N HIS* 1.3 94.0 + - + +
100N TYR* 1.3 63.6 + - - +
101N GLY* 5.0 5.6 - - - +
102N LYS* 5.6 1.1 - - + -
444N VAL* 4.5 8.5 - - + -
445N SER 4.5 4.5 - - - +
446N MET* 4.1 10.8 - - - -
458N TRP* 3.5 62.8 - - + +
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Residues in contact with TYR 100 (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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98N HIS* 5.0 5.4 - + + -
99N ILE* 1.3 75.9 - - - +
101N GLY* 1.3 57.6 + - - +
122N VAL* 3.9 7.9 - - + -
129N CYS* 3.1 35.2 - - - +
163N LEU* 3.5 31.0 - - + +
164N SER* 4.4 1.2 + - - -
410N PHE* 3.4 32.8 - + - -
412N ASP* 6.4 0.4 - - + -
445N SER* 2.9 35.6 + - - +
446N MET* 4.2 1.1 - - - -
447N CYS* 3.6 27.4 - - + +
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Residues in contact with GLY 101 (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* 4.8 3.6 - - - +
100N TYR* 1.3 81.2 - - - +
102N LYS* 1.3 61.2 + - - +
131N PHE* 4.3 5.3 - - - -
163N LEU* 4.6 7.0 - - - -
164N SER* 3.0 14.6 - - - -
444N VAL* 3.5 3.5 - - - +
445N SER* 2.8 39.5 + - - +
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Residues in contact with LYS 102 (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* 5.6 1.8 - - + -
101N GLY* 1.3 74.8 - - - +
103N ASP* 1.3 61.7 + - - +
104N ASN* 3.1 38.2 + - - +
131N PHE* 4.8 0.4 - - - -
164N SER* 2.9 21.2 + - - +
426N LEU* 5.0 1.8 - - - +
442N SER* 4.7 4.2 + - - -
443N ILE 3.4 14.6 - - - +
444N VAL* 4.3 9.0 - - + -
458N TRP* 3.8 46.7 - - + +
459N PRO* 2.3 35.2 + - - -
460N ASP* 3.8 6.5 + - - +
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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