Contacts of the helix formed by residues 42 - 62 (chain A) in PDB entry 2V32
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 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 2.5 40.2 + - + +
40A ASP 3.2 1.3 - - - +
41A PHE* 1.3 81.7 - - - +
43A PRO* 1.4 66.4 - - - +
44A VAL 3.7 0.4 - - - -
45A SER* 3.3 8.3 + - - -
46A THR* 2.6 37.7 + - - -
80A TRP* 4.1 1.0 - - - +
1222A BEZ 3.2 32.8 + - + -
187B PRO* 3.7 18.8 - - + -
212B TYR* 3.7 3.8 - - - -
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Residues in contact with PRO 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 1.4 85.0 - - - +
44A VAL* 1.3 64.4 + - - +
46A THR* 3.1 5.8 + - - +
47A THR* 3.1 23.4 + - - +
1222A BEZ 2.9 24.5 - - - +
184B MET* 3.8 29.8 - - + -
185B VAL 3.7 18.6 - - - +
187B PRO* 3.8 12.1 - - + -
212B TYR* 3.2 26.7 - - + +
213B LEU* 3.9 12.6 - - + +
214B ARG 4.5 0.4 - - - +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 1.3 76.7 - - - +
45A SER* 1.3 63.0 + - - +
47A THR* 2.8 22.7 + - - -
48A GLU* 3.1 11.6 + - + +
128A ARG* 3.6 24.7 - - - +
150A GLY* 3.8 15.0 - - - +
1222A BEZ 3.1 12.8 + - - +
172B ALA* 3.7 34.3 - - + +
173B THR 3.4 29.2 - - - +
174B PRO* 3.9 4.3 - - + -
184B MET* 3.7 12.3 - - + -
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A HIS* 3.4 17.7 - - - +
38A PRO* 3.4 14.7 - - - +
39A ARG 3.9 6.9 + - - -
42A THR* 3.3 23.6 + - - -
43A PRO 3.2 0.4 - - - -
44A VAL* 1.3 77.1 - - - +
46A THR* 1.3 55.7 + - - +
48A GLU* 3.1 6.1 + - - +
49A LEU* 3.0 32.6 + - - +
80A TRP* 3.8 5.4 - - - -
128A ARG* 2.8 26.0 + - - +
1222A BEZ 3.1 5.1 + - - -
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR 2.6 23.8 + - - -
43A PRO* 3.1 5.4 + - - -
45A SER* 1.3 73.4 - - - +
47A THR* 1.3 60.1 + - - +
49A LEU* 4.0 0.3 - - - +
50A GLY* 3.0 26.0 + - - -
80A TRP* 3.0 22.5 + - - -
83A ASP* 4.0 6.3 - - + +
84A VAL* 4.0 27.3 - - + +
87A LEU* 3.7 21.9 - - + +
212B TYR* 3.3 20.4 - - + +
213B LEU* 4.6 4.5 - - + -
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO 3.1 15.0 + - - +
44A VAL 2.8 17.2 + - - -
46A THR* 1.3 74.9 - - - +
48A GLU* 1.3 56.8 + - - +
50A GLY* 3.8 0.9 - - - -
51A ARG* 2.9 27.9 + - - +
87A LEU* 3.9 20.9 - - + -
174B PRO* 3.5 17.7 - - + +
175B ALA* 3.0 29.5 + - - +
184B MET* 4.6 13.5 - - + -
213B LEU* 4.9 0.2 - - + -
215B TYR* 4.7 7.2 - - + +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A HIS* 4.6 0.2 - - - +
44A VAL* 3.1 16.3 + - + +
45A SER* 3.1 7.1 + - - +
47A THR* 1.3 74.0 - - - +
49A LEU* 1.3 69.1 + - + +
51A ARG* 3.1 4.9 + - - +
52A VAL* 3.0 28.1 + - - +
128A ARG* 2.8 32.1 + - - -
150A GLY* 4.1 2.9 - - - -
151A ARG* 2.7 67.5 + - - +
153A PHE* 3.9 12.5 - - + -
175B ALA* 3.9 21.5 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.6 26.5 - - + -
37A HIS* 3.9 26.2 - - + +
45A SER 3.0 21.5 + - - +
48A GLU* 1.3 79.2 - - + +
50A GLY* 1.3 60.7 + - - +
52A VAL* 3.5 3.3 + - - -
53A ILE* 3.2 15.6 + - - +
68A ALA* 4.2 2.5 - - + -
80A TRP* 3.5 27.6 - - + -
84A VAL* 3.6 20.4 - - + -
94A MET* 5.0 0.2 - - + -
96A TYR* 2.7 35.6 + - + +
98A ILE* 4.0 21.5 - - + -
151A ARG* 5.0 0.4 - - - +
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Residues in contact with GLY 50 (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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46A THR 3.0 17.9 + - - -
47A THR* 3.9 1.6 - - - -
49A LEU* 1.3 75.1 - - - +
51A ARG* 1.3 63.4 + - - +
53A ILE 3.2 2.6 + - - -
54A GLN* 3.1 21.8 + - - +
84A VAL* 3.6 10.6 - - - +
87A LEU* 5.0 1.6 - - - -
88A SER* 3.3 32.9 - - - -
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR 2.9 22.3 + - - +
48A GLU* 3.1 5.6 + - - +
50A GLY* 1.3 72.7 - - - +
52A VAL* 1.3 62.0 + - - +
54A GLN* 2.7 50.8 + - - +
55A LEU* 3.1 57.6 + - + +
153A PHE* 4.3 13.7 - - + +
154A SER* 5.4 9.1 - - - +
175B ALA* 4.1 9.2 - - + -
176B ASP* 3.0 30.2 + - - +
180C GLY* 3.1 30.8 + - - -
181C ASP* 5.0 3.6 + - - +
217C PRO* 5.7 1.6 - - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.9 16.6 - - + -
48A GLU 3.0 18.3 + - - +
49A LEU 3.8 7.4 - - - +
50A GLY 3.2 0.2 - - - -
51A ARG* 1.3 72.1 - - - +
53A ILE* 1.3 68.2 + - - +
55A LEU* 3.1 17.2 + - - +
56A GLU* 3.1 12.6 + - - +
59A PHE* 4.9 3.4 - - + -
66A LEU* 3.7 33.7 - - + -
96A TYR* 3.4 24.9 - - + +
153A PHE* 3.8 36.1 - - + -
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Residues in contact with ILE 53 (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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49A LEU 3.2 9.1 + - - +
50A GLY 3.2 8.1 + - - +
52A VAL* 1.3 77.2 - - - +
54A GLN* 1.3 62.2 + - - +
56A GLU* 3.3 18.1 + - + +
84A VAL* 3.7 28.0 - - + -
85A LYS* 4.2 11.0 - - + -
88A SER* 3.8 13.7 - - - +
90A VAL* 3.5 39.0 - - + +
93A ASP 6.0 0.4 - - - +
94A MET* 3.8 20.2 - - - -
95A PRO* 3.8 29.8 - - + -
96A TYR* 4.0 5.4 - - - +
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Residues in contact with GLN 54 (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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50A GLY 3.1 15.7 + - - +
51A ARG* 2.7 53.3 + - - +
53A ILE* 1.3 77.3 - - - +
55A LEU* 1.3 57.8 + - - +
56A GLU 3.3 2.6 + - - -
57A GLY 4.9 1.7 + - - -
58A ASP* 5.0 1.6 - - - +
87A LEU 4.4 3.8 + - - -
88A SER* 3.3 35.3 + - - +
90A VAL* 4.4 11.4 - - + -
217C PRO* 3.5 34.0 - - + +
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Residues in contact with LEU 55 (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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51A ARG* 3.1 53.1 + - + +
52A VAL* 3.1 7.4 + - - +
54A GLN* 1.3 74.8 - - - +
56A GLU* 1.3 64.0 + - - +
57A GLY 3.3 2.2 - - - -
58A ASP* 3.1 33.2 + - - +
59A PHE* 3.1 29.5 + - + -
153A PHE* 3.6 33.7 - - + -
154A SER* 4.9 2.5 - - - +
157A LEU* 4.0 18.2 - - + -
180C GLY* 5.8 4.3 - - - -
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Residues in contact with GLU 56 (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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52A VAL 3.1 8.6 + - - +
53A ILE* 3.3 20.7 + - + +
54A GLN 3.3 1.4 - - - +
55A LEU* 1.3 79.9 - - - +
57A GLY* 1.3 70.9 + - - +
59A PHE* 3.4 8.1 + - - +
60A LYS* 2.9 39.6 + - - +
66A LEU* 4.7 8.6 - - + +
90A VAL* 6.4 0.9 - - + -
95A PRO* 3.6 38.7 - - + +
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Residues in contact with GLY 57 (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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54A GLN 4.9 2.2 + - - -
55A LEU 3.3 0.2 - - - -
56A GLU* 1.3 93.5 + - - +
58A ASP* 1.3 52.6 + - - +
60A LYS* 3.7 8.0 - - - +
61A LYS* 2.8 42.4 + - - +
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Residues in contact with ASP 58 (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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54A GLN 5.0 0.9 - - - +
55A LEU* 3.1 34.8 + - - +
57A GLY* 1.3 73.3 - - - +
59A PHE* 1.3 64.3 + - - +
61A LYS* 3.6 6.5 + - - +
62A ARG* 2.6 47.4 + - - +
157A LEU* 4.0 18.4 - - + +
180C GLY* 6.0 1.7 - - - -
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Residues in contact with PHE 59 (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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33A VAL* 4.4 2.7 - - + -
52A VAL* 4.9 6.5 - - + -
55A LEU* 3.1 45.0 + - + -
56A GLU 3.8 2.9 - - - +
58A ASP* 1.3 74.0 - - - +
60A LYS* 1.3 65.2 + - - +
62A ARG* 2.9 14.5 + - - +
64A VAL* 3.0 44.0 + - + +
66A LEU* 3.6 42.4 - - + -
153A PHE* 4.8 13.5 - + - -
156A ILE* 4.2 15.3 - - + -
157A LEU* 3.9 20.6 - - + -
160A ILE* 3.4 33.2 - - + -
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Residues in contact with LYS 60 (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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56A GLU* 2.9 32.7 + - - +
57A GLY* 3.7 7.6 - - - +
58A ASP 3.5 0.2 - - - -
59A PHE* 1.3 74.2 - - - +
61A LYS* 1.3 63.4 + - + +
63A GLY* 3.1 14.5 + - - +
64A VAL 4.4 4.9 + - - +
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Residues in contact with LYS 61 (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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57A GLY* 2.8 31.9 + - - +
58A ASP* 3.7 13.7 - - - +
59A PHE 3.2 0.6 - - - -
60A LYS* 1.3 71.8 - - - +
62A ARG* 1.3 66.2 + - + +
63A GLY 3.4 0.8 + - - -
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Residues in contact with ARG 62 (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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31A TRP* 5.1 0.3 - - - -
58A ASP* 2.6 53.6 + - - +
59A PHE* 2.9 8.3 + - - +
61A LYS* 1.3 86.0 - - + +
63A GLY* 1.3 56.9 + - - +
64A VAL* 3.3 9.4 - - + -
157A LEU* 3.7 26.6 + - - +
160A ILE* 3.8 11.7 - - + -
161A ASP* 2.9 39.4 + - - +
164A GLN* 2.7 44.2 + - - +
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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
------------------------------------------------------------
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