Contacts of the helix formed by residues 91 - 104 (chain A) in PDB entry 3NUI
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 ASP 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A GLN* 5.0 1.4 + - - -
78A ARG* 2.8 35.2 + - - -
79A PHE* 5.1 0.5 - - - -
90A SER* 1.3 74.7 - - - +
92A GLN* 1.3 81.7 + - - +
94A VAL* 3.1 5.2 + - - +
95A MET* 2.9 38.5 + - + +
32B VAL* 3.6 22.2 - - + +
33B VAL 2.8 16.6 + - - +
34B THR* 3.8 15.3 - - + +
44B VAL* 4.7 3.1 - - + -
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Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 3.3 33.6 + - - +
78A ARG* 4.0 8.5 - - - +
90A SER* 3.2 7.3 - - - +
91A ASP* 1.3 102.4 + - - +
93A THR* 1.3 65.6 + - - +
95A MET* 3.2 26.1 + - - +
96A LEU* 2.9 27.0 + - - +
327A PRO* 3.7 15.5 - - + +
330A CYS* 3.7 19.8 - - + +
331A ALA* 3.4 21.0 - - - +
334A LEU* 3.7 6.4 - - - +
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Residues in contact with THR 93 (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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84A ALA* 4.5 14.1 - - + +
89A MET* 3.8 30.9 - - + +
90A SER* 3.0 24.1 + - - -
92A GLN* 1.3 75.7 - - - +
94A VAL* 1.3 64.9 + - - +
97A SER* 2.9 33.3 + - - +
113A TYR* 3.8 21.9 + - + -
326A HIS 5.7 0.9 + - - -
327A PRO* 5.5 1.6 - - - +
330A CYS* 4.0 18.8 - - - +
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Residues in contact with VAL 94 (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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89A MET* 3.7 24.9 - - + -
90A SER 3.1 13.1 + - - +
91A ASP* 3.1 8.9 + - - +
93A THR* 1.3 83.4 - - - +
95A MET* 1.3 66.7 + - + +
97A SER* 3.8 5.0 - - - -
98A GLU* 3.3 25.4 + - + +
32B VAL* 4.1 23.6 - - + -
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Residues in contact with MET 95 (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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91A ASP* 2.9 28.5 + - + +
92A GLN* 3.2 37.2 + - - +
94A VAL* 1.3 80.6 - - + +
96A LEU* 1.3 58.3 + - - +
98A GLU* 3.4 7.8 + - - +
99A LYS* 3.0 27.0 + - - +
334A LEU* 3.8 20.2 - - + +
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Residues in contact with LEU 96 (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 GLN 2.9 17.2 + - - +
93A THR 4.2 0.7 - - - +
95A MET* 1.3 77.1 - - - +
97A SER* 1.3 54.8 + - - +
99A LYS* 3.1 0.8 + - + -
100A LEU* 2.7 44.3 + - + +
113A TYR* 3.5 31.4 - - + +
287A LEU* 4.8 1.8 - - + -
294A MET* 3.8 12.3 - - + -
330A CYS* 3.9 10.8 - - + -
333A ALA* 3.7 29.2 - - + -
334A LEU* 3.7 22.4 - - + +
337A ILE* 3.7 29.8 - - + -
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Residues in contact with SER 97 (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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93A THR* 2.9 20.4 + - - +
94A VAL* 3.8 6.5 - - - -
95A MET 3.3 0.2 - - - -
96A LEU* 1.3 76.8 - - - +
98A GLU* 1.3 63.8 + - - +
100A LEU 3.3 0.2 + - - -
101A VAL* 3.0 29.0 + - - +
111A VAL* 3.6 26.1 + - - +
113A TYR* 2.8 29.9 + - - -
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Residues in contact with GLU 98 (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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94A VAL* 3.3 14.4 + - + +
95A MET* 3.8 8.9 - - - +
97A SER* 1.3 78.1 - - - +
99A LYS* 1.3 62.7 + - - +
101A VAL* 3.5 5.1 + - - +
102A GLU* 3.1 24.8 + - + +
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Residues in contact with LYS 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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95A MET 3.0 17.2 + - - +
96A LEU* 3.7 4.3 - - + +
98A GLU* 1.3 77.1 - - - +
100A LEU* 1.3 59.1 + - - +
102A GLU* 3.1 35.8 + - - +
103A VAL* 3.0 40.0 + - + +
334A LEU* 3.9 20.4 - - + +
337A ILE* 3.8 34.5 - - + -
342A ASN* 5.9 3.2 - - - +
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Residues in contact with LEU 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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96A LEU* 2.7 43.9 + - + +
97A SER 3.9 2.9 - - - +
99A LYS* 1.3 69.5 - - - +
101A VAL* 1.3 59.1 + - - +
103A VAL* 3.4 5.4 + - + +
104A SER* 2.9 32.1 + - - -
111A VAL* 4.0 8.7 - - + -
113A TYR* 3.9 21.8 - - + +
262A PHE* 3.6 32.5 - - + -
283A SER* 5.5 0.9 - - - +
287A LEU* 4.1 5.6 - - + -
296A ALA* 3.9 17.3 - - + -
298A ILE* 3.9 25.8 - - + +
337A ILE* 3.8 11.9 - - + -
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Residues in contact with VAL 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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97A SER 3.0 19.9 + - - +
98A GLU* 4.0 5.2 - - - +
100A LEU* 1.3 73.9 - - - +
102A GLU* 1.3 65.8 + - - +
104A SER* 2.6 26.2 + - - +
106A PHE* 3.6 7.7 - - + +
107A ASP 4.2 6.7 - - - +
108A SER* 3.7 33.4 - - - +
109A GLY* 3.8 26.2 - - - +
110A ARG 4.4 0.2 - - - +
111A VAL* 3.9 16.2 - - + -
298A ILE* 4.6 5.6 - - + -
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Residues in contact with GLU 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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98A GLU* 3.1 16.8 + - + +
99A LYS* 3.1 45.9 + - - +
101A VAL* 1.3 80.2 - - - +
103A VAL* 1.3 65.4 + - + +
104A SER 3.6 5.5 + - - +
106A PHE 5.0 1.3 - - - +
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Residues in contact with VAL 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 LYS* 3.0 36.5 + - + +
100A LEU* 3.8 11.4 - - + +
102A GLU* 1.3 82.7 - - + +
104A SER* 1.4 59.3 + - - +
262A PHE* 4.0 27.1 - - + -
268A THR* 3.9 7.0 + - + +
269A TRP* 2.8 29.8 + - + -
337A ILE* 4.4 5.2 - - + -
341A MET* 3.8 33.8 - - + +
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Residues in contact with SER 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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100A LEU 2.9 16.1 + - - -
101A VAL* 2.6 22.2 + - - +
102A GLU 3.7 5.7 - - - +
103A VAL* 1.4 81.2 - - - +
105A PRO* 1.4 70.4 - - - +
106A PHE* 2.9 37.7 + - - +
269A TRP* 3.5 8.7 - - - +
281A ILE* 4.7 0.4 - - - -
298A ILE* 4.0 15.0 - - - -
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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