Contacts of the helix formed by residues 93 - 110 (chain A) in PDB entry 2NZ2
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 LEU 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A PHE* 3.6 17.1 - - + -
72A PHE* 3.6 26.0 - - + +
73A ILE* 4.6 5.2 - - - -
76A ALA* 3.7 34.1 - - + -
88A LEU 4.0 2.7 - - - +
89A LEU* 2.9 28.8 + - + +
90A GLY 4.0 2.5 - - - +
92A SER* 1.3 78.4 + - - +
94A ALA* 1.3 60.5 + - - +
95A ARG 3.4 0.2 - - - -
96A PRO* 3.4 15.6 - - - +
97A CYS 4.1 0.5 + - - -
186A MET* 3.5 29.8 - - + -
317A PHE* 4.3 3.8 - - + -
321A VAL* 3.7 18.8 - - + -
326A TRP* 4.2 14.4 - - + -
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Residues in contact with ALA 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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38A ILE* 4.0 12.3 - - + -
68A PHE* 3.6 18.6 - - + -
90A GLY 3.8 0.6 + - - -
91A THR* 3.1 9.7 + - - +
93A LEU* 1.3 77.2 - - - +
95A ARG* 1.3 64.6 + - - +
97A CYS* 3.1 7.6 + - - +
98A ILE* 2.9 37.1 + - + +
184A ASN* 3.4 29.6 - - + +
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Residues in contact with ARG 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 THR* 3.3 20.8 - - - +
92A SER 4.3 0.2 - - - +
94A ALA* 1.3 80.2 - - - +
96A PRO* 1.4 58.4 - - + +
98A ILE* 3.1 22.3 + - - +
99A ALA* 2.7 38.2 + - - +
124A ASP* 2.9 46.2 + - + +
127A ARG* 3.7 27.6 - - + -
128A PHE* 3.8 32.0 - - + +
182A ASP* 2.8 38.1 + - - -
501A ASP 4.7 2.0 + - - -
502A CIR 4.6 0.6 - - - -
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Residues in contact with PRO 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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72A PHE* 3.7 20.2 - - + -
92A SER 3.3 18.4 - - - +
93A LEU* 3.4 15.9 - - - +
95A ARG* 1.4 89.6 - - + +
97A CYS* 1.3 57.9 + - - +
99A ALA* 4.0 1.3 - - + -
100A ARG* 3.0 30.1 + - - +
127A ARG* 5.2 4.4 - - + +
131A SER* 3.8 16.2 - - - +
321A VAL* 5.8 0.9 - - + -
326A TRP* 3.8 26.0 - - + -
327A HIS* 3.4 15.9 + - - +
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Residues in contact with CYS 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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34A TYR* 4.5 0.2 + - - -
38A ILE* 4.3 2.2 - - + -
64A VAL* 3.3 36.3 - - - +
67A GLU* 4.2 8.8 - - - +
68A PHE* 3.9 27.6 - - + -
72A PHE* 3.8 32.0 - - + -
93A LEU 4.2 3.1 - - - +
94A ALA 3.1 14.5 + - - +
96A PRO* 1.3 84.3 - - - +
98A ILE* 1.3 59.9 + - - +
100A ARG* 4.2 7.8 + - - +
101A LYS* 3.7 17.0 + - - +
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Residues in contact with ILE 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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10A ALA* 4.8 6.3 - - + -
34A TYR* 2.8 40.8 + - + +
36A ALA* 3.8 20.6 - - + -
38A ILE* 4.3 21.8 - - + -
64A VAL* 5.3 0.9 - - + -
94A ALA* 2.9 31.1 + - + +
95A ARG* 3.6 31.9 - - - +
97A CYS* 1.3 75.5 - - - +
99A ALA* 1.3 65.3 + - - +
100A ARG 3.3 0.2 + - - -
101A LYS 3.4 1.2 + - - -
102A GLN* 3.1 12.9 + - - +
128A PHE* 3.6 19.1 - - + -
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Residues in contact with ALA 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 ARG 2.7 19.4 + - - +
96A PRO* 4.4 0.4 - - + -
98A ILE* 1.3 73.5 - - - +
100A ARG* 1.3 56.8 + - - +
102A GLN* 3.2 13.5 + - - +
103A VAL* 2.9 34.6 + - - +
128A PHE* 3.6 35.2 - - + +
131A SER* 3.7 18.4 - - - -
132A CYS* 4.3 3.8 - - - -
135A LEU* 5.1 0.2 - - - -
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Residues in contact with ARG 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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67A GLU* 3.1 30.2 + - - +
71A GLU* 2.8 44.1 + - - -
72A PHE* 3.5 28.4 - - - -
96A PRO 3.0 18.8 + - - +
97A CYS* 4.2 7.2 + - - +
98A ILE 3.3 0.2 - - - -
99A ALA* 1.3 77.9 - - - +
101A LYS* 1.3 57.8 + - - +
103A VAL* 3.6 4.3 + - - +
104A GLU* 3.1 29.9 + - - +
135A LEU* 4.0 25.7 - - + +
327A HIS* 4.0 12.7 - - - +
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Residues in contact with LYS 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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34A TYR* 3.3 22.0 - - + +
62A GLU* 3.7 38.7 + - + -
64A VAL* 4.2 20.0 - - + -
67A GLU* 4.5 15.0 + - - +
97A CYS 3.7 8.8 + - - +
98A ILE 3.4 2.1 + - - +
100A ARG* 1.3 77.9 - - - +
102A GLN* 1.3 60.2 + - - +
104A GLU* 2.8 34.8 + - + +
105A ILE* 3.0 40.9 + - + +
108A ARG* 5.1 4.2 - - - +
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Residues in contact with GLN 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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8A VAL* 3.2 26.4 + - + +
10A ALA* 3.4 19.7 - - - +
34A TYR* 3.6 20.7 + - + -
98A ILE 3.1 12.3 + - - +
99A ALA* 3.2 19.0 + - - +
101A LYS* 1.3 75.2 - - - +
103A VAL* 1.3 60.4 - - - +
105A ILE* 3.2 6.7 + - - +
106A ALA* 2.9 28.7 + - - +
114A VAL* 3.8 13.4 - - + +
115A SER 2.9 33.3 + - - +
116A HIS* 5.3 0.7 - - - +
128A PHE* 4.4 9.0 - - - +
132A CYS* 4.2 9.2 - - - -
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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 ALA 2.9 19.7 + - - +
100A ARG* 3.8 7.0 - - - +
102A GLN* 1.3 73.7 - - - +
104A GLU* 1.3 57.5 + - - +
106A ALA* 3.2 6.5 + - - +
107A GLN* 2.9 47.7 + - + +
114A VAL* 4.9 4.0 - - + +
131A SER 4.7 2.0 - - - +
132A CYS* 3.6 41.7 - - + +
135A LEU* 4.2 15.7 - - + -
136A ALA* 3.8 24.5 - - + -
139A ILE* 4.9 4.7 - - + -
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Residues in contact with GLU 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 ARG* 3.1 20.9 + - - +
101A LYS* 2.8 41.3 + - + +
102A GLN 3.2 0.2 - - - -
103A VAL* 1.3 77.5 - - - +
105A ILE* 1.3 61.9 + - - +
107A GLN* 4.2 6.1 - - - +
108A ARG* 3.2 42.1 + - - +
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Residues in contact with ILE 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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8A VAL* 4.3 17.0 - - + -
34A TYR* 3.3 39.3 - - + -
60A PHE* 3.8 42.2 - - + -
62A GLU* 3.9 16.2 - - + +
101A LYS* 3.0 24.6 + - + +
102A GLN* 3.2 5.1 + - - +
104A GLU* 1.3 73.2 - - - +
106A ALA* 1.3 59.8 + - - +
108A ARG* 3.5 25.6 + - - +
109A GLU* 3.0 29.9 + - + +
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Residues in contact with ALA 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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8A VAL* 3.9 18.4 - - + +
102A GLN 2.9 17.2 + - - +
103A VAL* 3.2 6.2 + - - +
105A ILE* 1.3 78.1 - - - +
107A GLN* 1.3 57.7 + - - +
109A GLU 3.5 0.5 + - - -
110A GLY 3.0 6.4 + - - -
111A ALA* 2.9 43.9 + - + +
113A TYR 4.7 0.4 - - - +
114A VAL* 3.9 22.0 - - + -
139A ILE* 4.8 7.2 - - + -
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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 VAL* 2.9 33.4 + - + +
104A GLU* 4.3 5.6 - - - +
106A ALA* 1.3 76.1 - - + +
108A ARG* 1.3 65.6 + - - +
110A GLY* 3.6 9.2 + - - +
111A ALA 5.3 1.1 - - - +
135A LEU 4.7 4.0 + - - +
136A ALA* 3.4 25.6 - - + +
139A ILE* 5.4 2.5 - - + -
503A NA 3.4 19.1 - - - -
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Residues in contact with ARG 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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60A PHE* 3.7 32.1 - - - -
62A GLU* 5.1 5.7 + - - -
101A LYS* 5.1 5.1 - - - +
104A GLU* 3.2 44.0 + - - +
105A ILE* 3.6 20.9 - - - +
106A ALA 3.3 0.2 - - - -
107A GLN* 1.3 79.7 - - - +
109A GLU* 1.3 67.3 + - - +
110A GLY 3.4 0.7 + - - -
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Residues in contact with GLU 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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6A SER* 5.5 0.9 - - - +
32A ILE* 4.0 27.7 - - + +
57A LYS* 4.6 3.8 + - - -
58A LYS* 3.3 38.8 + - - +
60A PHE* 3.7 25.3 - - + -
105A ILE* 3.0 21.2 + - + +
106A ALA 3.9 3.1 - - - +
108A ARG* 1.3 84.2 - - + +
110A GLY* 1.3 60.9 + - - +
111A ALA* 3.6 4.2 + - + +
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Residues in contact with GLY 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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6A SER* 5.4 1.5 - - - -
106A ALA 3.0 4.9 + - - -
107A GLN* 3.6 7.3 + - - -
108A ARG 3.2 4.8 + - - -
109A GLU* 1.3 79.8 - - - +
111A ALA* 1.3 61.6 + - - +
112A LYS* 3.8 8.7 + - - +
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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