Contacts of the helix formed by residues 98 - 110 (chain A) in PDB entry 3EHN
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ASN* 3.3 28.8 + - - +
96A ASN* 2.7 36.5 + - - +
97A PHE* 1.3 75.6 - - - +
99A ASP* 1.3 65.3 + - - +
100A SER* 3.6 7.1 + - - -
101A ARG* 3.3 26.9 + - - +
102A MET* 2.9 22.5 + - - +
504A ARG* 4.5 2.7 - - - +
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Residues in contact with ASP 99 (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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97A PHE 3.9 0.2 + - - -
98A THR* 1.3 72.9 - - - +
100A SER* 1.3 62.4 + - - +
103A ASN* 3.2 16.6 + - - -
504A ARG* 4.3 4.6 - - - +
506A ALA* 3.1 29.2 - - - +
507A PRO* 2.8 35.5 - - + +
508A THR* 2.6 43.9 + - - +
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Residues in contact with SER 100 (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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98A THR* 3.3 8.8 + - - -
99A ASP* 1.3 76.7 + - - +
101A ARG* 1.3 77.4 + - - +
103A ASN* 3.3 8.8 + - - +
104A TYR* 3.1 22.5 + - - +
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Residues in contact with ARG 101 (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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64A ASN 5.1 0.4 + - - -
67A GLN* 5.3 0.8 + - - -
68A ASN* 3.6 25.2 + - - +
72A ILE* 4.3 9.9 - - - +
90A ASN 4.4 2.5 - - - +
91A ASN* 3.8 18.3 - - + +
92A GLU* 2.5 47.5 + - - +
98A THR* 3.3 23.4 + - - +
100A SER* 1.3 88.7 + - - +
102A MET* 1.3 66.1 + - + +
104A TYR* 3.5 23.3 + - - +
105A ALA* 3.1 25.5 + - - +
1C NDG 3.0 38.2 + - - +
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Residues in contact with MET 102 (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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92A GLU* 4.2 15.3 - - + +
97A PHE* 3.5 48.2 - - + +
98A THR 2.9 20.2 + - - +
101A ARG* 1.3 84.4 - - + +
103A ASN* 1.3 60.7 + - - +
104A TYR 3.1 0.2 - - - -
105A ALA* 3.7 4.2 - - + +
106A TYR* 3.0 27.4 + - - +
154A PHE* 4.2 5.4 - - - -
503A PHE* 3.8 31.2 - - + -
504A ARG* 3.2 31.2 - - + +
506A ALA* 3.8 19.7 + - + +
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Residues in contact with ASN 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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99A ASP* 3.2 38.0 + - - +
100A SER* 3.6 7.4 - - - +
102A MET* 1.3 77.0 - - - +
104A TYR* 1.3 53.3 + - - +
106A TYR* 3.5 11.4 + - - +
107A GLN* 2.7 44.4 + - - +
506A ALA* 3.5 13.1 - - - +
508A THR* 3.6 8.5 + - - -
509A ALA* 4.4 12.2 - - - +
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Residues in contact with TYR 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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64A ASN* 3.0 28.2 + - + +
65A ASP* 2.7 27.9 + - - -
68A ASN* 3.6 33.9 - - + -
100A SER 3.1 15.3 + - - +
101A ARG* 3.6 31.2 - - - +
103A ASN* 1.3 76.4 - - - +
105A ALA* 1.3 58.3 + - - +
107A GLN* 3.1 21.9 + - + +
108A ASN* 2.8 51.5 + - - -
1C NDG 5.3 1.3 - - + -
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Residues in contact with ALA 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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68A ASN* 3.1 21.7 + - - +
101A ARG 3.1 15.4 + - - +
102A MET* 3.7 8.5 - - + +
104A TYR* 1.3 76.1 - - - +
106A TYR* 1.3 57.8 + - - +
108A ASN* 3.3 0.6 + - - +
109A PHE* 2.9 40.2 + - + -
154A PHE* 3.8 14.6 - - + -
503A PHE* 3.9 23.8 - - + -
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Residues in contact with TYR 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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102A MET 3.0 17.0 + - - +
103A ASN* 3.6 13.7 - - - +
104A TYR 3.2 0.2 - - - -
105A ALA* 1.3 76.6 - - - +
107A GLN* 1.3 60.3 + - + +
110A TYR* 2.9 69.1 + + + +
111A SER* 3.2 20.8 + - - -
154A PHE* 3.6 17.0 - + + -
157A ILE* 5.9 4.9 - - + -
158A ALA* 5.2 2.3 + - - +
171A PHE* 4.0 23.1 - + - -
505A PHE* 4.1 32.8 - + + -
516A MET* 6.0 1.8 - - + -
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Residues in contact with GLN 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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103A ASN* 2.7 28.1 + - - +
104A TYR* 3.1 28.3 + - - +
106A TYR* 1.3 80.6 - - + +
108A ASN* 1.3 65.2 + - - +
109A PHE 3.3 0.3 + - - -
110A TYR 3.7 0.7 + - - -
111A SER* 3.0 18.3 + - - +
112A GLN* 2.9 44.8 + - + +
113A ILE 4.7 0.2 + - - -
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Residues in contact with ASN 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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49A ARG* 4.1 15.9 - - - +
50A VAL 5.2 1.6 - - - +
52A PRO* 4.9 8.3 - - + +
65A ASP* 2.7 36.5 + - - +
68A ASN* 3.0 25.6 + - - +
69A THR* 3.5 22.6 - - + +
104A TYR* 2.8 46.0 + - - +
105A ALA 3.3 3.1 + - - +
107A GLN* 1.3 79.8 - - - +
109A PHE* 1.3 59.2 + - - +
112A GLN* 4.7 8.5 - - - +
113A ILE* 6.2 0.2 - - - +
149A ARG* 5.8 0.7 + - - -
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Residues in contact with PHE 109 (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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69A THR* 3.4 42.6 - - + -
105A ALA* 2.9 32.1 + - + +
108A ASN* 1.3 77.5 - - - +
110A TYR* 1.3 60.5 + - + +
113A ILE* 4.7 3.5 - - - +
146A ALA* 3.7 16.3 - - - +
147A TRP* 3.9 6.2 - - - -
149A ARG* 3.6 51.4 - - + -
150A ALA* 3.7 24.3 - - + +
153A VAL* 3.8 31.2 - - + -
154A PHE* 4.1 15.0 - + + -
464A VAL* 4.0 5.4 - - + -
467A TRP* 5.8 1.1 - + - -
503A PHE* 4.2 12.6 - + - -
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Residues in contact with TYR 110 (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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106A TYR* 2.9 53.1 + + + +
107A GLN 3.7 0.4 + - - -
109A PHE* 1.3 80.6 - - + +
111A SER* 1.3 72.6 + - - +
112A GLN 3.5 1.8 - - - -
113A ILE* 3.5 4.3 - - - +
114A PHE* 3.3 29.5 + + + +
147A TRP* 3.3 61.1 + + - +
150A ALA* 4.3 9.6 - - + -
154A PHE* 6.1 0.4 - - + -
157A ILE* 4.5 15.3 - - + -
158A ALA* 2.7 44.2 + - + +
162A ALA* 4.4 3.6 - - - +
169A PRO* 5.8 0.5 - - - +
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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