Contacts of the helix formed by residues 50 - 65 (chain A) in PDB entry 4FJV
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 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASP* 2.8 37.3 + - - +
49A GLY* 1.3 78.4 - - - +
51A CYS* 1.3 65.8 + - - +
52A PHE 3.2 2.7 - - - -
53A TYR* 3.0 8.2 + - - -
54A ARG* 3.0 37.2 + - - +
129A ASP* 4.6 1.2 + - - -
132A VAL* 4.1 10.3 - - + -
136A ARG* 2.8 22.3 + - - +
171A MET* 3.4 22.3 - - - +
172A ALA* 2.8 29.3 + - - +
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Residues in contact with CYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.4 25.4 + - - +
46A LYS 3.7 12.1 - - - +
48A ASP* 3.7 2.3 + - - -
49A GLY 3.4 0.8 - - - -
50A ASN* 1.3 77.2 - - - +
52A PHE* 1.3 64.4 + - - +
54A ARG* 4.1 3.2 - - - +
55A ALA* 3.0 27.2 + - - +
224A HIS* 3.8 4.3 - - + -
225A TYR* 3.5 25.4 - - - +
75B GLY 3.9 2.5 - - - -
101B NEH 1.8 53.2 - - + -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 5.3 0.2 + - - -
50A ASN 3.2 0.8 - - - -
51A CYS* 1.3 81.2 - - - +
53A TYR* 1.3 73.7 + + + +
55A ALA* 3.4 1.7 + - - +
56A LEU* 3.0 47.1 + - + +
175A CYS* 3.4 38.8 - - + -
180A ILE* 3.8 41.7 - - + -
183A LEU* 4.1 21.1 - - + -
191A LEU* 3.9 15.5 - - + -
193A VAL* 5.7 0.2 - - + -
218A LEU* 3.7 27.1 - - + -
225A TYR* 4.0 21.3 - + + -
75B GLY 4.8 1.3 + - - +
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 5.0 0.7 - - - -
50A ASN* 3.0 8.1 + - - +
52A PHE* 1.3 86.1 - + + +
54A ARG* 1.3 64.1 + - - +
56A LEU* 3.4 1.9 + - - +
57A GLY* 3.1 19.4 + - - -
132A VAL* 4.0 18.8 - - + -
135A LEU* 3.6 22.8 - - + +
136A ARG* 3.2 62.2 + - + -
139A THR* 3.9 18.4 - - - -
167A GLU 4.8 0.3 + - - -
168A VAL* 4.3 8.0 + - - +
173A THR 4.2 2.5 - - - -
175A CYS* 3.9 21.4 - - + +
179A GLN* 3.4 31.9 + - + +
183A LEU* 3.7 21.5 - - + -
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Residues in contact with ARG 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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8A LEU* 3.9 43.0 + - - +
9A ILE* 4.2 11.0 - - + -
45A THR* 5.3 2.4 - - - -
46A LYS* 5.2 4.2 + - - +
48A ASP* 2.7 33.9 + - - -
50A ASN* 3.0 26.4 + - - +
51A CYS* 4.1 4.2 - - - +
53A TYR* 1.3 78.8 - - - +
55A ALA* 1.3 55.9 - - - +
57A GLY* 3.9 0.3 - - - -
58A TYR* 2.9 31.0 + - - +
122A PHE* 4.0 14.2 - - + -
125A GLN* 4.6 0.6 - - - +
128A SER* 2.7 47.4 + - - +
129A ASP* 3.1 28.7 + - - -
132A VAL* 3.8 16.8 - - + +
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Residues in contact with ALA 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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9A ILE* 4.7 0.2 - - - -
45A THR* 3.8 18.1 - - + +
51A CYS 3.0 20.3 + - - +
52A PHE* 3.7 5.6 - - - +
53A TYR 3.3 0.2 - - - -
54A ARG* 1.3 75.1 - - - +
56A LEU* 1.3 59.8 + - - +
59A SER* 2.9 34.5 + - - -
218A LEU* 4.0 22.2 - - + -
225A TYR 4.3 6.5 - - - +
227A ILE* 3.8 15.0 - - + +
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Residues in contact with LEU 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 PHE* 3.0 34.3 + - + +
53A TYR* 4.0 3.1 - - - +
55A ALA* 1.3 73.1 - - - +
57A GLY* 1.3 62.2 - - - +
59A SER* 4.3 0.2 - - - -
60A TYR* 2.9 35.2 + - - +
135A LEU* 6.0 1.1 - - + -
183A LEU* 3.7 35.7 - - + -
184A SER* 5.0 5.4 - - - +
187A LEU* 5.9 0.2 - - + -
189A ILE* 4.2 35.0 - - + -
191A LEU* 3.7 39.0 - - + -
216A VAL* 4.0 13.0 - - + -
218A LEU* 4.7 1.8 - - + -
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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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53A TYR 3.1 15.5 + - - -
54A ARG 3.9 0.7 - - - -
56A LEU* 1.3 77.7 - - - +
58A TYR* 1.3 62.4 + - - +
60A TYR* 4.0 2.4 - - - +
61A LEU* 3.1 30.4 + - - +
102A PHE* 5.3 6.5 - - - -
122A PHE* 3.7 12.1 - - - -
135A LEU* 4.2 16.2 - - - +
189A ILE* 6.0 2.0 - - - -
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Residues in contact with TYR 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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9A ILE* 4.0 15.9 - - + -
43A ARG* 3.6 17.8 + - - -
54A ARG 2.9 18.9 + - - +
55A ALA 4.2 1.3 - - - +
57A GLY* 1.3 76.1 - - - +
59A SER* 1.3 58.8 + - - +
61A LEU* 3.7 1.0 - - - +
62A GLU* 2.8 74.5 + - + +
115A VAL* 3.4 11.6 - - - +
118A LEU* 3.6 21.8 - - + -
119A LEU* 3.4 37.6 - - + +
122A PHE* 3.6 42.6 - + + -
227A ILE* 4.0 14.1 - - + -
229A TYR* 4.0 0.2 - - - -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA 2.9 19.4 + - - -
58A TYR* 1.3 82.0 - - - +
60A TYR* 1.3 57.8 + - - +
62A GLU* 3.5 9.4 + - - +
63A SER* 2.9 28.2 + - - -
215A SER 4.6 1.7 + - - -
216A VAL* 3.6 28.7 - - - +
217A TYR 4.7 1.2 + - - -
227A ILE* 3.7 29.1 - - - +
228A LEU 5.2 0.9 + - - -
229A TYR* 5.7 0.7 - - - -
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU 2.9 19.6 + - - +
57A GLY* 4.2 1.8 - - - +
59A SER* 1.3 78.3 - - - +
61A LEU* 1.3 64.5 + - + +
63A SER* 2.7 24.9 + - - -
64A LEU* 3.3 40.0 + - + +
70A GLU* 5.0 0.9 + - - +
74A PHE* 3.5 48.4 - + - +
102A PHE* 6.1 0.7 - + - -
187A LEU 5.2 0.9 + - - -
188A SER 5.3 2.9 + - - -
189A ILE* 3.4 39.7 - - + -
215A SER* 3.3 27.1 - - - -
216A VAL* 3.6 11.6 - - + +
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Residues in contact with LEU 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 3.1 20.6 + - - +
58A TYR 3.8 2.5 - - - +
60A TYR* 1.3 75.2 - - + +
62A GLU* 1.3 67.4 + - - +
64A LEU* 3.0 37.3 + - + +
65A LEU* 3.5 8.8 + - - +
74A PHE* 4.3 8.5 - - + -
102A PHE* 4.3 12.3 - - + -
105A VAL* 3.5 36.3 - - + +
106A VAL* 4.2 21.5 - - + -
109A VAL* 4.0 16.3 - - + +
118A LEU* 3.8 12.1 - - + -
122A PHE* 3.9 16.8 - - + -
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Residues in contact with GLU 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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12A LYS* 5.6 1.0 + - - -
43A ARG* 3.4 11.1 + - - -
58A TYR* 2.8 54.8 + - + +
59A SER* 3.7 10.0 + - - +
61A LEU* 1.3 74.7 - - - +
63A SER* 1.3 59.3 + - - +
64A LEU 3.1 0.9 + - - -
65A LEU* 3.4 29.5 + - + +
115A VAL* 3.9 10.9 - - + +
118A LEU* 3.4 13.6 - - + +
229A TYR* 2.9 39.4 + - - -
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Residues in contact with SER 63 (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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59A SER 2.9 15.5 + - - -
60A TYR* 2.7 34.3 + - - -
61A LEU 3.1 0.4 - - - -
62A GLU* 1.3 76.3 - - - +
64A LEU* 1.3 58.0 + - - +
65A LEU 3.5 1.3 - - - +
67A LYS* 3.0 36.9 + - - +
215A SER* 3.9 26.1 - - - -
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Residues in contact with LEU 64 (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 TYR* 3.4 52.5 - - + +
61A LEU* 3.0 24.1 + - + +
63A SER* 1.3 81.8 - - - +
65A LEU* 1.3 66.7 + - - +
66A GLY 3.1 0.5 + - - -
67A LYS* 2.8 24.6 + - + +
70A GLU* 4.0 31.9 - - + -
71A ILE* 3.4 24.2 - - + +
74A PHE* 3.8 21.1 - - + -
106A VAL* 6.2 1.1 - - + -
109A VAL* 4.0 5.2 - - + -
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Residues in contact with LEU 65 (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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61A LEU 3.5 6.5 + - - +
62A GLU* 3.4 27.0 + - + +
63A SER 4.6 1.6 - - - +
64A LEU* 1.3 76.6 - - - +
66A GLY* 1.3 61.5 + - - +
67A LYS* 3.5 6.6 + - - +
108A LEU* 5.8 0.2 - - + -
109A VAL* 3.9 29.8 - - + +
113A GLY* 3.5 33.0 - - - +
114A SER* 3.9 4.0 - - - +
115A VAL* 3.6 43.5 - - + +
118A LEU* 4.4 5.4 - - + -
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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