Contacts of the helix formed by residues 52 - 71 (chain A) in PDB entry 1VH2
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 ASP 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ALA 3.7 3.0 + - - -
51A ILE* 1.3 76.2 - - - +
53A PRO* 1.3 79.6 - - - +
54A ALA* 3.3 28.1 + - - +
55A ALA* 3.1 13.4 + - + +
56A ILE* 3.0 20.3 + - - +
83A ARG* 4.2 1.3 - - - +
132A ASP* 5.2 4.2 - - - +
135A ALA* 5.9 2.2 - - + -
139A HIS* 4.8 3.0 + - - +
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Residues in contact with PRO 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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51A ILE 3.5 0.4 - - - +
52A ASP* 1.3 96.3 - - - +
54A ALA* 1.3 60.5 + - - +
56A ILE* 3.4 11.3 - - + +
57A HIS* 3.0 25.1 + - - +
83A ARG* 3.9 28.5 - - - +
130A ASP* 3.8 13.1 - - - +
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.3 15.1 + - - +
53A PRO* 1.3 78.2 - - - +
55A ALA* 1.3 58.7 + - - +
57A HIS* 3.2 3.5 + - - +
58A THR* 3.0 30.3 + - - -
130A ASP* 3.5 28.3 + - - +
131A HIS* 3.7 24.9 - - - +
132A ASP* 3.6 8.3 + - + -
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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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51A ILE* 3.8 13.9 - - + -
52A ASP* 3.1 17.6 + - + +
54A ALA* 1.3 81.0 - - - +
56A ILE* 1.3 57.4 + - - +
58A THR* 3.3 3.0 + - - +
59A LEU* 2.9 30.2 + - - +
132A ASP* 4.0 12.7 - - + +
135A ALA* 3.8 28.5 - - + -
136A ALA* 4.0 6.5 - - - +
139A HIS* 4.3 5.8 - - + -
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Residues in contact with ILE 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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51A ILE* 3.6 23.5 - - + +
52A ASP 3.0 10.8 + - - +
53A PRO* 3.4 15.9 - - + +
55A ALA* 1.3 73.9 - - - +
57A HIS* 1.3 65.8 + - - +
59A LEU* 3.5 5.0 - - + +
60A GLU* 2.8 28.1 + - - +
79A PRO* 3.7 27.4 - - + +
80A MET 4.2 0.2 - - - +
83A ARG* 3.7 44.0 - - + -
85A GLY 3.8 15.5 - - - +
86A MET* 3.7 17.3 - - - +
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Residues in contact with HIS 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 PRO 3.0 18.9 + - - +
54A ALA 3.3 6.3 - - - +
55A ALA 3.2 0.2 - - - -
56A ILE* 1.3 79.5 - - - +
58A THR* 1.3 61.9 + - - +
60A GLU* 3.2 19.4 + - - +
61A HIS* 3.1 19.0 + + - -
79A PRO* 6.1 0.9 - - - -
125A CYS* 3.5 2.5 - - - -
127A ASN* 3.2 33.8 + - + +
130A ASP* 2.6 25.5 + - - +
131A HIS* 3.2 12.1 + + - -
167A ZN 2.2 36.3 - - - -
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Residues in contact with THR 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 ALA 3.0 4.1 + - - -
55A ALA 3.6 7.4 - - - -
57A HIS* 1.3 78.1 - - - +
59A LEU* 1.3 62.3 + - - +
61A HIS* 3.1 3.9 + - - +
62A LEU* 3.0 31.1 + - + +
117A ILE* 3.7 28.7 - - + -
131A HIS* 3.0 18.4 + - - +
132A ASP 2.8 29.5 + - - -
133A LEU* 4.0 6.7 - - - -
136A ALA* 3.6 21.5 - - + -
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Residues in contact with LEU 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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43A PHE* 3.8 35.4 - - + -
51A ILE* 4.2 21.5 - - + -
55A ALA 2.9 19.0 + - - +
56A ILE* 3.5 17.7 - - + +
57A HIS 3.3 0.2 - - - -
58A THR* 1.3 76.8 - - - +
60A GLU* 1.3 62.6 + - - +
62A LEU* 4.6 3.6 - - - +
63A LEU* 2.9 37.1 + - + +
86A MET* 4.2 11.7 - - + -
107A LEU* 5.7 0.4 - - + -
110A THR* 4.1 16.2 - - + -
136A ALA* 3.6 31.4 - - + +
139A HIS* 4.6 6.7 - - + -
140A ALA* 5.2 0.4 - - + +
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Residues in contact with GLU 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 ILE 2.8 14.4 + - - +
57A HIS* 3.3 30.8 + - - +
58A THR 3.1 0.2 - - - -
59A LEU* 1.3 76.9 - - - +
61A HIS* 1.3 71.1 + - + +
63A LEU* 4.4 0.8 - - - +
64A ALA* 3.2 25.2 + - + +
77A VAL* 3.9 19.3 - - - +
78A SER* 4.9 1.4 + - - -
79A PRO* 3.5 25.0 - - + +
86A MET* 3.8 14.6 - - + +
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Residues in contact with HIS 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 HIS* 3.1 16.7 + + - +
58A THR* 3.1 9.7 + - - +
60A GLU* 1.3 88.7 - - + +
62A LEU* 1.3 61.7 + - - +
64A ALA* 3.7 14.3 + - - +
65A GLY 4.1 2.1 + - - -
117A ILE* 3.9 13.2 - - + -
118A PRO* 2.6 33.2 + - + +
119A GLY* 3.2 28.3 - - - -
120A VAL* 4.1 0.8 - - - +
124A GLU 5.1 2.2 + - - -
125A CYS* 4.0 1.1 - - + -
131A HIS* 3.7 18.3 - + - -
167A ZN 2.2 36.3 - - - -
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Residues in contact with LEU 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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58A THR* 3.0 29.4 + - + +
59A LEU* 4.0 2.7 - - - +
61A HIS* 1.3 74.9 - - - +
63A LEU* 1.3 61.7 + - + +
65A GLY* 3.4 3.5 + - - -
66A TYR* 3.0 42.2 + - + -
110A THR* 3.7 29.6 - - + +
113A HIS* 3.6 43.3 - - + +
117A ILE* 4.8 2.2 - - + -
118A PRO* 3.6 20.2 - - + -
133A LEU* 4.0 22.7 - - + -
136A ALA* 4.5 4.3 - - + -
137A ARG* 5.5 0.2 - - + -
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Residues in contact with LEU 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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41A LEU* 5.8 0.7 - - + -
43A PHE* 4.2 17.3 - - + -
59A LEU* 2.9 28.1 + - + +
60A GLU 4.4 0.4 - - - +
62A LEU* 1.3 72.9 - - + +
64A ALA* 1.3 67.1 + - - +
65A GLY 3.1 2.2 - - - -
66A TYR* 4.2 2.2 - - + +
67A MET* 2.9 34.3 + - + +
77A VAL* 3.9 18.1 - - + +
86A MET* 4.0 26.5 - - + -
103A PHE* 4.5 9.4 - - + -
106A ALA* 4.0 26.0 - - + +
107A LEU* 4.7 7.0 - - + -
110A THR* 3.6 23.1 - - - +
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Residues in contact with ALA 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 GLU* 3.2 19.4 + - + +
61A HIS* 3.7 9.2 - - - +
62A LEU 3.3 0.4 - - - -
63A LEU* 1.3 77.8 - - - +
65A GLY* 1.3 60.7 + - - +
67A MET* 4.7 0.3 - - - +
68A ARG* 2.7 46.4 + - - +
76A ASP* 5.7 2.2 - - - +
77A VAL* 4.5 12.1 - - + +
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Residues in contact with GLY 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 HIS 4.1 2.8 + - - -
62A LEU 3.4 5.1 + - - -
63A LEU 3.1 0.2 - - - -
64A ALA* 1.3 80.4 - - - +
66A TYR* 1.3 60.3 + - - +
67A MET 3.3 0.4 - - - -
68A ARG* 3.2 8.7 + - - +
69A ASP* 3.0 34.1 + - - +
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Residues in contact with TYR 66 (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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62A LEU* 3.0 31.0 + - + +
63A LEU* 4.4 3.1 - - - -
65A GLY* 1.3 76.0 - - - +
67A MET* 1.3 62.7 + - - +
69A ASP* 3.2 22.4 + - - +
70A HIS* 3.1 25.6 - - - -
106A ALA* 3.7 20.2 - - + +
109A ASP* 3.5 46.1 + - + +
110A THR* 3.6 18.6 - - - -
113A HIS* 2.5 38.1 + + - -
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Residues in contact with MET 67 (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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41A LEU* 4.8 3.6 - - + -
63A LEU* 2.9 30.8 + - + +
64A ALA 4.7 0.7 - - - +
66A TYR* 1.3 76.2 - - - +
68A ARG* 1.3 58.1 + - - +
70A HIS* 3.0 3.9 + - - +
71A LEU* 2.8 44.9 + - + +
74A VAL* 4.6 4.5 - - + -
77A VAL* 4.0 22.2 - - + -
88A MET* 3.7 33.0 - - + -
99A VAL 4.5 1.3 - - - +
102A ALA* 4.1 5.8 - - + +
103A PHE* 3.7 41.1 - - + +
106A ALA* 3.4 21.8 - - + -
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Residues in contact with ARG 68 (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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64A ALA* 2.7 47.8 + - - +
65A GLY* 3.2 11.5 + - - +
67A MET* 1.3 79.0 - - - +
69A ASP* 1.3 62.6 + - - +
70A HIS 3.3 0.2 + - - -
71A LEU 3.5 18.0 + - - +
74A VAL* 4.0 31.1 + - + +
75A VAL 3.1 18.8 + - - -
76A ASP* 3.0 28.1 + - - +
77A VAL 5.1 0.6 - - - +
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Residues in contact with ASP 69 (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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65A GLY 3.0 17.4 + - - +
66A TYR* 3.5 34.7 - - - +
67A MET 3.1 0.4 - - - -
68A ARG* 1.3 79.2 - - - +
70A HIS* 1.3 76.3 + - + +
109A ASP* 4.7 0.9 - - - +
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Residues in contact with HIS 70 (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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66A TYR 3.1 21.5 + - - +
67A MET 3.0 4.2 + - - +
69A ASP* 1.3 90.0 + - + +
71A LEU* 1.3 61.4 + - - +
102A ALA* 3.5 28.2 - - + +
105A ALA* 3.6 20.6 - - + +
106A ALA 3.6 17.7 - - - -
109A ASP* 2.6 30.4 + - - -
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Residues in contact with LEU 71 (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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67A MET* 2.8 20.1 + - + +
68A ARG* 3.5 17.0 + - - +
70A HIS* 1.3 83.0 - - - +
72A GLU* 1.3 76.7 + - - +
74A VAL* 3.5 25.1 + - + +
88A MET* 3.7 29.8 - - + -
90A VAL* 4.1 13.2 - - + -
98A GLY 4.9 3.8 - - - +
99A VAL* 4.3 21.3 - - + +
102A ALA* 3.7 12.8 - - + -
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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