Contacts of the helix formed by residues 77 - 95 (chain N) in PDB entry 1VQ7
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 ASN 77 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30499 G 3.3 19.1 - - - +
30509 G 3.0 37.3 + - - +
43N VAL* 5.3 0.5 - - - +
71N TRP* 4.8 3.8 - - - -
73N ALA* 5.7 0.6 - - - +
74N PRO* 3.6 23.7 + - - +
76N GLY* 1.3 75.4 - - - +
78N MET* 1.3 68.7 + - - +
79N PRO* 3.5 12.2 - - + +
80N SER* 2.9 36.3 + - - -
81N ALA* 2.9 21.8 + - - +
114N LYS* 3.7 7.1 - - - +
146N HIS* 5.4 0.2 - - - +
147N ILE* 4.9 3.3 - - + +
159N TYR* 4.2 4.0 + - - -
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Residues in contact with MET 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30489 C 4.2 6.1 - - - +
30499 G 3.0 20.0 + - - +
77N ASN* 1.3 75.4 - - - +
79N PRO* 1.3 70.2 - - + +
81N ALA* 2.9 3.8 + - - +
82N TYR* 2.9 24.1 + - - +
112N GLY 3.1 28.5 - - - +
113N SER* 3.8 10.8 - - - +
114N LYS* 3.5 24.9 - - - +
117N ALA* 4.2 14.1 - - + +
137N ALA* 3.5 22.2 - - + +
141N ARG* 3.6 27.1 - - + +
142N THR* 3.8 12.3 - - - +
146N HIS* 3.8 9.4 - - + -
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Residues in contact with PRO 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71N TRP* 4.3 14.1 - - + -
77N ASN* 3.5 17.7 - - + +
78N MET* 1.3 93.2 - - + +
80N SER* 1.3 60.6 + - - +
82N TYR* 4.7 0.4 - - + -
83N LEU* 3.1 34.6 + - - +
142N THR 3.0 16.5 - - - +
143N ARG 3.0 30.1 - - - +
144N GLY* 3.5 11.0 - - - -
146N HIS* 4.5 2.5 - - + -
147N ILE* 5.8 2.2 - - + -
172N PHE* 3.7 16.0 - - + -
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Residues in contact with SER 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N VAL* 5.1 2.1 - - - +
63N SER* 3.6 10.0 - - - -
66N LEU* 3.9 12.5 - - - +
71N TRP* 4.7 4.2 - - - -
74N PRO 4.5 2.2 - - - -
75N THR* 3.0 34.6 + - - +
77N ASN* 2.9 38.9 + - - -
79N PRO* 1.3 77.8 - - - +
81N ALA* 1.3 51.0 + - - +
83N LEU* 3.8 2.1 - - - +
84N THR* 2.6 36.6 + - - -
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Residues in contact with ALA 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N VAL* 4.0 17.4 - - + +
77N ASN 2.9 12.3 + - - +
78N MET 2.9 8.0 + - - +
80N SER* 1.3 73.8 - - - +
82N TYR* 1.3 68.3 + - - +
84N THR* 3.0 2.8 + - - -
85N GLY* 2.8 21.1 + - - -
114N LYS* 3.7 36.1 - - + +
117N ALA* 3.9 4.7 - - + -
118N ILE* 4.0 13.6 - - + +
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Residues in contact with TYR 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78N MET 2.9 12.9 + - - +
79N PRO 3.9 3.6 - - - +
81N ALA* 1.3 73.0 - - - +
83N LEU* 1.3 65.5 + - + +
85N GLY* 3.0 1.9 + - - -
86N LEU* 2.9 45.5 + - + +
117N ALA* 3.6 16.4 - - + +
120N GLU* 3.7 16.2 - - + -
121N GLY* 3.6 18.8 - - - -
124N ASP* 2.8 33.7 + - + +
139N TRP* 3.8 9.4 - + - -
142N THR* 3.3 34.8 - - + -
172N PHE* 3.8 15.3 - + + -
176N ARG* 2.7 40.5 + - - -
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Residues in contact with LEU 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N LEU* 3.9 18.6 - - + -
71N TRP* 3.5 23.6 - - + -
79N PRO 3.1 18.7 + - - +
80N SER 3.8 2.9 - - - +
82N TYR* 1.3 88.5 - - + +
84N THR* 1.3 57.1 + - - +
86N LEU* 3.1 4.4 + - + +
87N LEU* 2.8 31.9 + - - +
172N PHE* 3.6 26.5 - - + -
175N LEU* 3.4 25.1 - - + -
176N ARG* 3.9 29.6 - - + +
179N LEU* 4.3 11.1 - - + +
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Residues in contact with THR 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N VAL* 3.4 30.9 - - + +
45N ALA* 4.3 7.0 - - + +
61N ALA* 3.3 31.5 - - + +
62N HIS 3.9 1.7 + - - +
63N SER* 3.5 23.3 - - - +
66N LEU* 4.2 6.9 - - - +
80N SER 2.6 24.4 + - - -
81N ALA* 3.5 4.2 - - - -
83N LEU* 1.3 76.5 - - - +
85N GLY* 1.3 57.8 + - - +
87N LEU* 4.4 4.5 - - - -
88N ALA* 3.0 25.1 + - - +
118N ILE* 5.5 0.2 - - - -
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Residues in contact with GLY 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N ALA* 4.4 3.6 - - - -
81N ALA 2.8 12.3 + - - -
82N TYR 3.4 4.0 - - - -
84N THR* 1.3 77.6 - - - +
86N LEU* 1.3 51.4 + - - +
88N ALA* 3.4 2.3 + - - +
89N GLY 2.8 30.0 + - - -
118N ILE* 3.6 31.3 - - - +
122N ALA* 3.5 17.0 - - - +
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Residues in contact with LEU 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N TYR* 2.9 31.8 + - + +
83N LEU* 3.5 7.6 - - + +
85N GLY* 1.3 72.8 - - - +
87N LEU* 1.3 65.1 + - - +
89N GLY 3.3 0.2 + - - -
90N LEU* 3.0 44.7 + - + +
121N GLY* 3.4 15.1 - - - +
124N ASP* 4.1 7.0 - - + +
125N ALA* 3.4 31.3 - - + +
176N ARG* 4.5 4.9 - - + -
179N LEU* 3.6 20.9 - - + -
180N LEU* 3.4 32.8 - - + -
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Residues in contact with LEU 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N ALA* 3.9 5.4 - - + -
62N HIS 5.0 1.3 - - - +
65N ASP* 3.7 22.2 - - - +
66N LEU* 4.3 15.5 - - + -
69N TYR* 4.3 16.4 - - + +
83N LEU 2.8 20.3 + - - +
84N THR* 3.8 5.8 - - - +
86N LEU* 1.3 73.7 - - - +
88N ALA* 1.3 64.0 + - - +
90N LEU* 3.0 18.8 + - - +
91N ARG* 3.1 57.3 + - - +
179N LEU* 4.5 16.4 - - + +
186N LEU* 4.2 17.7 - - + -
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Residues in contact with ALA 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N LEU* 5.4 5.4 - - + -
45N ALA* 3.6 28.9 - - + +
46N GLN* 5.5 0.9 - - - -
47N LEU* 5.1 4.2 - - + +
59N ALA* 4.3 5.1 - - - +
60N SER* 4.0 9.0 - - - -
61N ALA* 3.3 25.7 - - + +
84N THR 3.0 13.0 + - - +
85N GLY 3.7 2.9 - - - +
87N LEU* 1.3 76.2 - - - +
89N GLY* 1.3 57.6 + - - +
91N ARG* 3.5 2.7 + - - +
92N ALA* 3.0 28.9 + - - +
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Residues in contact with GLY 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N LEU* 6.3 0.4 - - - -
47N LEU* 6.0 0.4 - - - -
85N GLY 2.8 18.2 + - - -
86N LEU 3.6 1.6 - - - -
87N LEU 3.1 0.4 - - - -
88N ALA* 1.3 77.4 - - - +
90N LEU* 1.3 56.2 + - - +
92N ALA* 3.1 9.7 + - - +
93N GLN* 2.8 31.6 + - - +
122N ALA* 4.4 8.7 - - - +
125N ALA* 3.6 15.5 - - - -
127N LEU* 4.4 10.2 - - - +
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Residues in contact with LEU 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N LEU* 3.0 25.1 + - + +
87N LEU* 3.0 7.6 + - - +
89N GLY* 1.3 75.2 - - - +
91N ARG* 1.3 61.7 + - - +
93N GLN* 3.2 10.2 + - + +
94N GLU* 2.9 21.5 + - - +
125N ALA* 3.6 28.7 - - + +
179N LEU* 3.8 42.6 - - + +
180N LEU* 5.7 3.6 - - + -
186N LEU* 3.8 31.5 - - + +
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Residues in contact with ARG 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N ALA* 4.1 11.4 - - + -
60N SER 3.0 28.2 + - - +
61N ALA* 3.5 10.5 - - - +
65N ASP* 3.0 28.3 + - - -
68N GLU* 4.9 5.7 + - - -
69N TYR* 3.5 23.0 + - - -
87N LEU* 3.1 35.9 + - + +
88N ALA* 3.7 5.4 - - - +
90N LEU* 1.3 74.8 - - - +
92N ALA* 1.3 64.4 + - - +
94N GLU* 2.9 19.5 + - - +
95N ALA* 3.0 13.3 + - - +
186N LEU* 3.4 34.7 + - + +
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Residues in contact with ALA 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N LEU* 3.4 35.4 - - + -
59N ALA* 3.5 13.4 - - + +
88N ALA 3.0 15.0 + - - +
89N GLY* 3.2 12.3 - - - +
91N ARG* 1.3 76.0 - - - +
93N GLN* 1.3 64.3 + - - +
95N ALA* 2.9 14.0 + - - +
97N VAL* 3.2 25.1 + - + +
127N LEU* 4.2 5.2 - - + -
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Residues in contact with GLN 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89N GLY 2.8 18.2 + - - +
90N LEU* 3.2 11.9 - - + +
92N ALA* 1.3 72.2 - - - +
94N GLU* 1.3 62.0 - - - +
96N GLY* 3.1 15.4 + - - -
97N VAL 2.9 27.2 + - - +
98N GLU* 4.0 10.9 + - - +
125N ALA 3.5 22.4 - - - +
126N GLY* 3.5 21.3 + - - +
127N LEU* 3.5 13.8 - - + +
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Residues in contact with GLU 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90N LEU 2.9 6.5 + - - +
91N ARG* 2.9 15.1 + - - +
93N GLN* 1.3 75.4 - - - +
95N ALA* 1.3 57.6 + - - +
96N GLY 3.2 1.1 + - - -
186N LEU* 3.5 32.3 - - + -
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Residues in contact with ALA 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58N LEU* 3.9 26.8 - - + +
91N ARG 3.0 10.1 + - - +
92N ALA* 2.9 11.4 + - - +
94N GLU* 1.3 75.5 - - - +
96N GLY* 1.3 56.9 + - - +
97N VAL* 3.3 12.6 + - + +
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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
------------------------------------------------------------
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