Contacts of the helix formed by residues 94 - 115 (chain A) in PDB entry 4NJP
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 GLY 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ARG* 3.8 4.9 + - - -
93A ALA* 1.3 72.4 - - - +
95A PRO* 1.3 71.5 - - - +
97A THR* 3.3 3.0 + - - -
98A TRP* 2.8 28.2 + - - +
163A GLY* 5.7 1.6 + - - -
166A GLU* 3.3 22.0 + - - +
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Residues in contact with PRO 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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94A GLY* 1.3 81.3 - - - +
96A VAL* 1.3 63.2 + - + +
98A TRP* 4.5 7.2 - - + -
99A VAL* 2.9 40.4 + - + +
166A GLU* 3.2 13.5 - - + +
171A SER* 3.9 10.3 - - - +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 1.3 75.5 - - + +
97A THR* 1.3 67.7 - - - +
99A VAL* 4.0 2.3 - - - +
100A MET* 3.1 26.2 + - + +
158A TRP* 4.4 8.1 - - + -
166A GLU* 2.9 20.6 + - - +
171A SER* 3.9 17.5 - - - +
174A LEU* 3.8 23.1 - - + -
175A ILE* 3.8 35.4 - - + +
178A THR* 5.5 1.3 - - + +
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Residues in contact with THR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.7 23.1 - - + -
94A GLY 3.4 5.6 - - - -
96A VAL* 1.3 77.5 - - - +
98A TRP* 1.3 62.7 + - - +
101A MET* 3.4 18.5 + - + +
158A TRP* 2.9 37.2 + - - +
159A TRP* 4.3 10.3 - - - -
162A GLY 3.6 6.2 + - - -
163A GLY* 3.4 31.3 + - - +
166A GLU* 2.5 23.3 + - - -
174A LEU* 3.7 2.3 - - - +
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Residues in contact with TRP 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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93A ALA* 4.0 12.6 - - + +
94A GLY 2.8 22.0 + - - +
95A PRO* 4.2 4.9 - - + +
97A THR* 1.3 71.7 - - - +
99A VAL* 1.3 75.7 + - + +
101A MET* 3.2 25.3 + - + +
102A ILE* 3.0 55.4 + - + +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 2.9 30.0 + - + +
96A VAL* 3.4 3.6 + - - +
98A TRP* 1.3 82.6 - - + +
100A MET* 1.3 65.2 + - - +
102A ILE* 3.3 11.9 + - + +
103A ALA* 2.8 26.8 + - + +
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Residues in contact with MET 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 3.1 10.1 + - + +
99A VAL* 1.3 78.1 - - - +
101A MET* 1.3 58.3 + - - +
103A ALA* 3.1 4.6 + - - +
104A CYS* 2.8 33.0 + - - -
142A ALA* 5.6 1.6 - - + -
143A LEU* 3.6 30.5 - - + -
158A TRP* 3.4 42.8 - - + +
178A THR* 3.7 30.1 - - + -
200A LEU* 3.8 34.8 - - + -
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Residues in contact with MET 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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93A ALA* 4.3 9.6 - - + -
97A THR* 3.4 28.4 + - + +
98A TRP* 3.2 33.3 + - + +
99A VAL 3.2 0.4 - - - -
100A MET* 1.3 78.4 - - - +
102A ILE* 1.3 64.5 + - - +
104A CYS* 3.2 2.4 + - - +
105A VAL* 3.0 29.4 + - + +
155A LEU* 4.0 27.4 - - + +
158A TRP* 3.5 17.9 - - + -
159A TRP* 4.0 32.3 - - + +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 3.0 67.7 + - + +
99A VAL* 3.5 13.9 - - + +
101A MET* 1.3 76.1 - - - +
103A ALA* 1.3 63.9 + - - +
105A VAL* 3.2 6.9 + - - +
106A VAL* 2.9 37.3 + - + +
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Residues in contact with ALA 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 VAL* 2.8 26.1 + - + +
100A MET* 3.7 6.1 - - - +
102A ILE* 1.3 76.9 - - + +
104A CYS* 1.3 57.7 + - - +
106A VAL* 3.7 5.1 - - - +
107A VAL* 3.0 35.7 + - + +
143A LEU* 4.4 22.2 - - + -
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Residues in contact with CYS 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 MET* 2.8 28.6 + - - +
101A MET 3.6 4.7 - - - +
102A ILE 3.2 0.2 - - - -
103A ALA* 1.3 77.4 - - - +
105A VAL* 1.3 56.4 + - - +
107A VAL* 3.6 1.6 + - - +
108A PHE* 2.9 30.7 + - - +
142A ALA 4.4 0.2 - - - -
143A LEU* 3.8 34.5 - - - +
145A HIS* 3.8 21.3 - - + -
151A ILE* 3.6 13.2 - - + +
155A LEU* 4.2 12.8 - - + -
200A LEU* 4.1 12.8 - - - -
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Residues in contact with VAL 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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101A MET* 3.0 21.0 + - + +
102A ILE* 3.5 9.9 - - - +
104A CYS* 1.3 74.3 - - - +
106A VAL* 1.3 63.0 - - + +
108A PHE* 3.2 4.1 + - + +
109A ILE* 2.9 50.8 + - + +
151A ILE* 4.2 8.3 - - + -
155A LEU* 4.3 15.9 - - + -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 2.9 33.4 + - + +
103A ALA* 3.7 6.1 - - - +
105A VAL* 1.3 78.1 - - + +
107A VAL* 1.3 64.4 + - + +
109A ILE* 3.3 13.5 + - + +
110A ALA* 2.9 29.2 + - + +
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Residues in contact with VAL 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 ALA* 3.0 21.0 + - + +
104A CYS 3.7 0.2 - - - +
106A VAL* 1.3 79.1 - - + +
108A PHE* 1.3 60.2 + - - +
110A ALA* 3.3 7.5 + - + +
111A MET* 2.8 31.0 + - - +
119A VAL* 4.2 3.4 - - + -
123A LEU* 4.0 23.3 - - + -
143A LEU* 3.3 40.6 - - + +
144A MET* 4.0 19.1 - - + -
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Residues in contact with PHE 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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104A CYS 2.9 21.8 + - - +
105A VAL* 3.2 6.7 + - + +
107A VAL* 1.3 73.9 - - - +
109A ILE* 1.3 61.3 + - + +
111A MET* 3.2 6.6 + - - -
112A GLN* 2.9 68.5 + - + +
145A HIS* 3.4 35.2 - - + +
146A PHE 4.5 1.6 - - - -
147A SER* 4.0 26.5 - - - -
148A LEU* 3.8 31.4 - - + -
151A ILE* 3.7 19.5 - - + -
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Residues in contact with ILE 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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105A VAL* 2.9 35.3 + - + +
106A VAL* 3.5 13.9 - - + +
108A PHE* 1.3 76.7 - - + +
110A ALA* 1.3 66.7 + - - +
112A GLN* 2.9 19.9 + - + +
113A ILE* 2.9 33.0 + - + +
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Residues in contact with ALA 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 VAL* 2.9 19.8 + - + +
107A VAL* 3.5 8.5 - - - +
109A ILE* 1.3 75.3 - - - +
111A MET* 1.3 56.7 + - - +
113A ILE* 3.4 7.1 + - - -
114A LEU* 2.9 44.1 + - + +
119A VAL* 3.8 13.9 - - + -
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Residues in contact with MET 111 (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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107A VAL* 2.8 21.8 + - - +
108A PHE* 3.5 9.6 - - - +
109A ILE 3.1 0.2 - - - -
110A ALA* 1.3 75.3 - - - +
112A GLN* 1.3 65.4 + - - +
115A GLY* 3.0 34.5 - - - -
116A ASP* 3.4 34.5 + - + +
119A VAL* 3.6 22.7 - - + -
144A MET* 3.9 23.6 - - + -
145A HIS 3.2 37.7 - - - +
146A PHE* 3.4 30.1 - - + -
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Residues in contact with GLN 112 (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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108A PHE* 2.9 67.1 + - + +
109A ILE* 2.9 12.1 + - + +
111A MET* 1.3 86.9 - - - +
113A ILE* 1.3 64.0 + - + +
115A GLY* 4.3 1.9 + - - -
116A ASP* 4.4 6.1 + - - +
146A PHE 5.9 0.6 + - - -
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Residues in contact with ILE 113 (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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109A ILE* 2.9 37.5 + - + +
110A ALA* 3.9 6.7 - - - +
112A GLN* 1.3 81.0 - - + +
114A LEU* 1.3 74.5 + - + +
115A GLY 3.3 0.4 + - - -
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Residues in contact with LEU 114 (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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110A ALA* 2.9 31.4 + - + +
113A ILE* 1.3 86.3 - - + +
115A GLY* 1.3 65.8 + - - +
118A GLU* 3.6 31.4 + - + +
119A VAL* 4.2 13.2 - - + -
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Residues in contact with GLY 115 (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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111A MET 3.0 17.7 + - - +
112A GLN 4.3 2.3 + - - -
113A ILE 3.3 2.8 + - - -
114A LEU* 1.3 82.8 - - - +
116A ASP* 1.3 66.0 + - - +
117A GLN* 3.3 3.3 + - - -
118A GLU 4.2 0.2 - - - -
119A VAL* 3.4 22.2 + - - +
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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