Contacts of the strand formed by residues 94 - 102 (chain N) in PDB entry 3H1I
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 GLN 94 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N TRP* 3.8 6.2 - - + -
41N ILE 3.9 10.1 - - - +
42N GLY 4.6 0.7 - - - -
43N ALA 3.2 13.5 + - - +
44N GLY* 4.1 0.2 - - - -
89N TYR* 3.1 29.8 + - + -
91N SER* 2.8 38.8 + - - +
92N ARG 3.8 0.4 - - - -
93N GLU* 1.3 81.6 - - - +
95N THR* 1.3 66.2 + - - +
377N GLU* 3.5 0.8 + - - -
381N SER* 2.4 29.5 + - - -
384N LEU* 4.0 16.2 - - + +
385N ASN* 3.2 27.0 + - - -
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Residues in contact with THR 95 (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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40N TRP 3.7 0.5 - - - -
41N ILE* 2.8 34.2 + - - +
43N ALA* 2.5 30.1 + - - -
44N GLY* 4.0 1.0 - - - -
56N GLY 4.6 5.2 - - - +
60N GLU* 5.0 0.4 - - + -
89N TYR* 2.8 27.8 - - - +
90N THR* 3.6 21.7 + - - +
94N GLN* 1.3 75.8 - - - +
96N ALA* 1.3 70.1 + - - +
97N PHE* 3.7 25.6 - - + -
185N TYR* 4.0 6.3 + - - +
190N PHE* 5.0 5.6 - - + -
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Residues in contact with ALA 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N VAL 3.3 10.3 - - - +
40N TRP* 2.9 42.4 - - + +
41N ILE 4.4 0.7 - - - +
88N GLY* 3.2 4.6 - - - -
89N TYR* 3.0 38.7 + - + +
95N THR* 1.3 84.2 - - - +
97N PHE* 1.3 68.2 + - - +
98N TYR* 4.2 2.2 - - + -
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Residues in contact with PHE 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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38N GLY* 3.3 1.2 - - - -
39N VAL* 2.9 39.9 + - + +
41N ILE* 4.1 22.2 - - + -
59N VAL* 4.5 2.2 - - + -
60N GLU* 3.9 27.6 - - + -
63N ALA* 3.3 31.4 - - + -
64N PHE* 3.9 20.9 - + - -
86N PHE* 3.8 18.4 - - + -
87N ASN 4.1 3.8 - - - -
88N GLY* 5.2 2.2 - - - -
95N THR* 3.7 28.0 - - + -
96N ALA* 1.3 78.1 - - - +
98N TYR* 1.3 60.8 + - - +
113N LEU* 4.0 5.2 - - + +
116N VAL* 5.2 4.9 - - + -
117N VAL* 4.9 8.3 - - + -
190N PHE* 4.2 14.6 - + - -
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Residues in contact with TYR 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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36N THR* 4.0 15.7 - - + -
37N VAL 3.2 14.6 - - - +
38N GLY* 3.5 9.9 - - - -
40N TRP* 3.9 29.8 - + + -
85N HIS 5.3 1.3 - - - -
86N PHE* 3.0 10.6 - - - -
87N ASN* 2.5 70.2 + - + +
88N GLY* 3.8 12.7 - - - -
89N TYR* 4.6 18.1 - + - -
96N ALA* 4.6 3.1 - - + -
97N PHE* 1.3 75.7 - - - +
99N ILE* 1.3 68.3 + - - +
100N LYS* 5.0 6.1 - - + -
113N LEU* 4.4 0.9 - - - -
373N THR* 3.6 26.3 - - + +
377N GLU* 5.5 0.9 - - + -
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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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36N THR* 3.1 6.5 - - - -
37N VAL* 2.7 37.3 + - - +
79N VAL* 5.1 6.7 - - + -
84N ALA* 3.4 30.1 - - + -
85N HIS 3.1 13.7 - - - +
86N PHE* 3.1 52.0 - - + -
98N TYR* 1.3 72.9 - - - +
100N LYS* 1.3 65.8 + - - +
101N ALA* 3.9 4.1 + - + +
109N VAL* 4.0 24.2 - - + +
112N LEU* 4.5 16.6 - - + -
113N LEU* 3.9 7.4 - - + -
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Residues in contact with LYS 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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35N CYS 3.4 6.2 + - - +
36N THR* 3.1 13.1 + - + +
83N GLY 4.4 1.0 - - - +
84N ALA* 3.0 5.9 - - - -
85N HIS* 2.8 49.5 + - + +
98N TYR* 5.0 7.4 - - + -
99N ILE* 1.3 71.9 - - - +
101N ALA* 1.3 60.2 + - - +
372N THR* 2.9 28.9 + - - -
373N THR* 3.1 22.5 + - + +
370O MET* 3.9 34.2 - - - +
373O GLU* 3.0 19.0 + - - -
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Residues in contact with ALA 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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34N THR* 3.9 5.5 + - - -
35N CYS* 2.7 46.2 + - - -
36N THR* 4.6 0.2 - - - +
83N GLY 5.2 1.8 - - - -
84N ALA* 3.4 21.3 - - + +
99N ILE* 3.9 4.3 + - + +
100N LYS* 1.3 75.9 - - - +
102N LEU* 1.3 64.8 + - - +
105N ASP* 4.5 7.0 - - + +
109N VAL* 4.0 25.6 - - + -
370O MET* 5.3 3.4 - - - -
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Residues in contact with LEU 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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33N PRO 4.0 6.3 - - - +
34N THR* 4.1 7.4 + - - +
35N CYS* 4.0 1.2 - - - -
82N MET 3.8 16.6 - - - +
83N GLY 5.6 1.6 - - - +
101N ALA* 1.3 76.4 - - + +
103N SER* 1.3 59.8 + - - +
104N LYS* 2.8 39.8 + - + +
105N ASP* 3.1 32.2 + - - +
106N MET 3.7 5.0 + - - -
362O ASN* 5.4 7.0 - - + +
365O LYS* 5.2 4.9 - - + -
366O ALA* 4.1 34.3 - - + +
369O LEU* 4.9 15.3 - - + -
370O MET* 6.4 0.4 - - + -
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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