Contacts of the helix formed by residues 99 - 117 (chain B) in PDB entry 2N5T
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 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASP* 2.7 38.8 + - + +
28B ARG* 4.5 1.6 - - - -
29B LYS 3.3 25.4 - - - +
31B ILE* 4.7 7.0 - - + -
39B GLU* 4.4 12.1 - - - +
93B ILE* 4.3 0.4 - - - -
98B MET* 1.3 76.9 - - - +
100B ALA* 1.3 55.6 + - - +
101B ASP* 2.7 22.5 + - - -
102B ALA* 2.8 21.3 - - + +
103B ALA* 2.6 37.5 + - - +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLU* 3.7 23.5 + - - +
42B ARG* 5.6 1.1 - - + -
43B PHE* 3.9 30.3 - - + +
89B ILE* 4.7 1.8 - - + -
93B ILE* 3.8 19.3 - - + +
98B MET 4.0 0.4 + - - -
99B THR* 1.3 75.3 - - - +
101B ASP* 1.3 58.3 + - - +
103B ALA* 4.4 0.4 - - - -
104B ALA* 2.8 35.0 + - - +
141B ILE* 4.6 12.1 - - + -
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL 4.5 1.3 - - - +
26B ILE* 3.6 11.2 - - + +
27B ASP* 3.8 22.3 + - - +
39B GLU* 5.9 0.4 - - - -
99B THR* 2.7 28.3 + - - -
100B ALA* 1.3 77.2 - - - +
102B ALA* 1.3 61.1 + - - -
104B ALA* 4.7 0.7 - - - -
105B HIS* 3.3 17.3 + - - +
138B LEU* 3.0 39.2 - - + +
141B ILE* 4.5 13.2 - - + +
142B LEU* 3.9 21.9 - - + +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.3 21.1 - - + -
27B ASP 4.4 1.3 - - - +
28B ARG* 5.2 5.6 - - + +
98B MET* 4.5 14.4 - - + +
99B THR* 2.8 24.1 + - + +
101B ASP* 1.3 82.4 + - - +
103B ALA* 1.3 63.1 + - - +
105B HIS* 3.5 5.4 + - - +
106B GLU* 3.4 19.4 + - - +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 4.0 7.2 - - + -
92B LEU* 4.2 16.7 - - + +
93B ILE* 3.7 22.4 - - + -
98B MET* 4.1 20.3 - - + +
99B THR 2.6 24.1 + - - +
102B ALA* 1.3 72.2 - - - +
104B ALA* 1.3 64.9 + - - +
106B GLU* 3.2 15.1 + - - +
107B VAL* 3.3 15.1 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 5.5 5.2 - - + -
89B ILE* 3.7 24.6 - - + +
100B ALA 2.8 24.9 + - - +
101B ASP* 4.5 2.7 - - - +
103B ALA* 1.3 74.9 - - - +
105B HIS* 1.3 62.8 + - - +
107B VAL* 3.2 13.0 + - - +
108B ILE* 3.3 19.1 + - + +
137B LEU* 6.1 5.8 - - + -
138B LEU* 4.9 9.2 - - + -
141B ILE* 4.9 8.5 - - + -
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 6.1 1.6 - - + -
26B ILE* 5.8 9.4 - - + -
101B ASP 3.3 19.3 + - - +
102B ALA* 3.7 7.2 - - - +
103B ALA 3.2 0.6 - - - -
104B ALA* 1.3 80.2 - - - +
106B GLU* 1.3 56.0 + - - +
108B ILE* 3.3 16.7 - - + +
109B GLU* 2.6 79.4 + - + +
131B ARG* 5.5 4.0 + - - -
134B GLY 5.5 1.6 - - - -
135B LYS* 6.0 3.3 - - - -
138B LEU* 4.5 21.5 - - + +
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 4.0 22.0 - - + +
96B LYS* 5.4 5.1 - - - +
98B MET* 3.9 22.9 - - - +
102B ALA 3.4 8.1 + - - +
103B ALA 3.2 9.1 + - - +
105B HIS* 1.3 81.9 + - - +
107B VAL* 1.3 54.6 + - - +
109B GLU* 4.3 8.5 - - - -
110B GLY* 2.6 33.6 + - - -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.1 36.4 - - + +
88B GLU* 4.2 15.0 - - + -
89B ILE* 4.2 22.4 - - + +
92B LEU* 3.9 20.2 - - + -
103B ALA 3.6 13.0 - - - +
104B ALA* 3.2 9.5 + - - +
106B GLU* 1.3 77.4 - - - +
108B ILE* 1.3 63.1 + - + +
110B GLY* 3.8 0.7 - - - -
111B GLN* 3.2 22.2 + - - +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 6.0 1.1 - - + -
85B LEU* 4.9 15.7 - - + -
104B ALA* 3.4 13.2 - - + +
105B HIS* 3.3 28.5 - - + +
107B VAL* 1.3 75.8 - - + +
109B GLU* 1.3 83.1 + - + +
111B GLN* 3.4 6.0 + - - +
112B ALA* 3.0 25.1 + - - +
130B VAL* 5.1 4.9 - - - +
131B ARG* 4.6 13.7 - - + +
133B ILE* 4.5 11.0 - - + -
134B GLY* 3.7 40.6 - - - +
135B LYS* 4.6 1.3 - - - +
137B LEU* 4.6 10.3 - - + -
138B LEU* 5.8 0.2 - - + -
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B HIS* 2.6 54.8 + - + +
106B GLU* 4.0 5.3 - - - +
108B ILE* 1.3 84.1 - - + +
110B GLY* 1.3 52.8 + - - +
112B ALA* 4.4 4.9 - - - -
113B SER* 2.5 52.5 + - - +
131B ARG* 4.4 15.9 + - - +
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Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU* 2.6 26.7 + - - -
107B VAL 3.8 0.9 - - - -
108B ILE 3.2 0.2 - - - -
109B GLU* 1.3 73.6 - - - +
111B GLN* 1.3 61.4 + - - +
113B SER* 3.5 6.7 - - - -
114B ALA* 3.1 20.8 + - - +
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 4.4 23.3 - - - +
85B LEU* 6.0 1.9 - - + +
107B VAL 3.2 12.4 + - - +
108B ILE* 4.0 7.8 - - - +
110B GLY* 1.3 71.7 - - - +
112B ALA* 1.3 69.7 + - - +
114B ALA* 2.8 18.5 + - + +
115B LEU* 3.0 24.2 + - + +
126B ARG* 6.2 2.0 - - - -
130B VAL* 4.9 15.9 - - + +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE 3.0 17.3 + - - +
109B GLU* 3.9 3.8 - - - +
111B GLN* 1.3 77.1 - - - +
113B SER* 1.3 64.2 + - - +
115B LEU* 3.0 16.9 + - - +
116B GLU* 3.0 13.2 + - - +
127B ALA* 4.2 9.1 - - + +
130B VAL* 3.5 30.2 - - + +
131B ARG* 4.1 28.0 + - + +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU* 2.5 45.4 + - - +
110B GLY* 3.5 7.6 - - - -
112B ALA* 1.3 74.4 - - - +
114B ALA* 1.3 61.5 + - - +
116B GLU* 3.3 16.7 + - - +
117B GLU* 3.4 16.8 + - - +
131B ARG* 4.7 7.2 + - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLY 3.1 11.9 + - - +
111B GLN* 2.8 13.7 + - + +
113B SER* 1.3 78.1 - - - +
115B LEU* 1.3 68.2 + - + +
117B GLU* 3.2 21.3 + - - +
118B LEU* 3.2 13.7 - - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLN* 3.5 25.4 - - + +
112B ALA* 3.0 11.2 + - - +
114B ALA* 1.3 82.4 - - + +
116B GLU* 1.3 62.9 + - - +
118B LEU* 2.8 39.2 + - + +
123B LEU* 4.4 21.8 - - + +
124B LYS* 5.1 4.4 - - - -
126B ARG* 5.1 16.2 - - + +
127B ALA* 3.5 24.7 - - + +
130B VAL* 5.9 2.0 - - + -
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 3.0 11.3 + - - +
113B SER* 3.3 11.7 + - - +
115B LEU* 1.3 76.2 - - - +
117B GLU* 1.3 80.7 + - - +
118B LEU 2.7 11.8 + - - +
124B LYS* 5.1 23.3 - - + +
127B ALA* 4.6 6.0 - - + +
131B ARG* 5.4 6.7 - - - +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B SER 3.5 13.9 - - - +
114B ALA* 3.3 16.2 - - - +
115B LEU 3.1 0.4 - - - -
116B GLU* 1.3 88.5 + - - +
118B LEU* 1.3 64.0 + - + +
119B ASP* 3.5 2.6 + - - +
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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
------------------------------------------------------------
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