Contacts of the strand formed by residues 48 - 66 (chain A) in PDB entry 2V72
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 GLN 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 2.6 35.9 + - - +
17A SER* 3.4 21.9 - - - +
36A TRP* 4.7 3.5 - - + -
38A THR* 3.9 22.2 - - + -
44A ASP* 3.6 30.8 - - - +
45A ALA 2.9 21.1 + - - +
46A LEU* 3.8 9.8 - - + +
47A PRO* 1.3 79.1 + - - +
49A SER* 1.3 61.5 + - - +
120A THR* 3.7 2.0 - - - -
121A ALA* 2.8 33.3 + - - +
129A ALA* 5.3 0.2 - - + -
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.4 6.6 - - - +
16A THR* 3.1 45.4 + - - +
36A TRP* 3.7 7.8 - - - -
48A GLN* 1.3 74.8 - - - +
50A LEU* 1.3 60.7 + - - +
51A SER* 4.2 1.8 + - - -
118A LYS* 3.3 27.5 - - - +
119A ILE 3.1 12.8 - - - -
120A THR* 3.5 19.7 - - - -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 4.2 4.3 - - + -
14A SER 3.4 16.6 - - - +
15A ALA* 4.3 3.1 - - + -
24A ALA* 3.6 33.7 - - + +
27A ALA* 3.8 21.1 - - + -
36A TRP* 3.9 24.0 - - + -
49A SER* 1.3 73.4 - - - +
51A SER* 1.3 65.3 + - - +
52A VAL* 4.1 17.3 + - + +
117A ILE 3.8 0.9 - - - +
118A LYS* 3.4 2.1 - - - -
119A ILE* 2.8 38.4 + - + +
131A ILE* 3.9 24.0 - - + -
134A LEU* 4.4 9.2 - - + -
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR 4.1 0.2 - - - +
13A ALA* 3.5 2.6 - - - +
14A SER* 2.7 48.3 + - - +
49A SER* 4.2 1.8 + - - -
50A LEU* 1.3 73.2 - - - +
52A VAL* 1.3 63.0 + - - +
53A ASN 4.1 0.4 - - - -
116A GLU* 3.8 21.4 + - - -
117A ILE 3.4 6.7 - - - -
118A LYS* 3.4 27.2 - - - +
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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
----------------------------------------------------------
11A MET* 3.9 29.2 - - + -
12A THR 3.5 7.2 - - - +
13A ALA* 4.5 4.5 - - + -
28A ILE* 4.2 15.0 - - + -
50A LEU* 4.1 24.9 - - + +
51A SER* 1.3 78.3 - - - +
53A ASN* 1.3 71.7 + - - +
54A LEU* 3.8 10.4 + - + +
116A GLU* 3.4 3.7 - - - -
117A ILE* 2.8 41.8 + - + +
119A ILE* 6.0 0.7 - - + -
134A LEU* 4.2 22.0 - - + -
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Residues in contact with ASN 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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11A MET* 3.2 28.6 - - - +
12A THR* 2.9 28.0 + - - +
51A SER 4.1 0.8 - - - -
52A VAL* 1.3 71.9 - - - +
54A LEU* 1.3 60.4 + - - +
55A GLY* 3.0 29.1 + - - -
115A GLU* 3.7 13.1 + - - +
116A GLU* 2.8 31.7 + - - +
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Residues in contact with LEU 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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6A ILE* 4.3 6.7 - - + +
10A GLU 3.5 10.2 - - - +
11A MET* 4.6 10.0 - - + +
52A VAL* 3.9 17.9 - - + +
53A ASN* 1.3 74.4 - - - +
55A GLY* 1.3 54.6 + - - +
56A LYS 3.3 3.4 - - - +
58A ARG* 3.2 43.9 + - + +
60A VAL* 4.1 11.0 - - + -
114A ALA* 3.3 26.0 - - + +
115A GLU 2.7 24.3 + - - +
116A GLU 4.0 3.4 - - - +
117A ILE* 3.9 22.7 - - + -
136A VAL* 3.9 30.3 - - + -
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 3.5 15.2 + - - -
53A ASN* 3.0 17.1 + - - -
54A LEU* 1.3 75.8 - - - +
56A LYS* 1.3 60.7 + - - +
58A ARG* 4.8 2.5 - - - -
115A GLU* 4.1 1.5 + - - -
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Residues in contact with LYS 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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10A GLU* 5.4 0.9 - - - +
54A LEU* 3.3 3.7 - - - +
55A GLY* 1.3 76.6 - - - +
57A ALA* 1.3 79.4 + - - +
58A ARG* 3.4 51.2 + - - +
115A GLU* 3.5 21.1 + - - -
138A GLU* 4.8 4.2 + - - -
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Residues in contact with ALA 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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56A LYS* 1.3 93.0 + - - +
58A ARG* 1.3 60.2 + - - +
85A ASN* 4.5 12.3 - - - +
113A ASP* 6.4 0.7 - - + -
114A ALA 4.1 4.3 - - - -
115A GLU* 4.5 8.4 - - + +
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Residues in contact with ARG 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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6A ILE* 3.6 29.7 - - + +
7A PRO* 4.9 3.4 - - - +
10A GLU* 2.6 32.3 + - - +
54A LEU* 3.2 31.9 + - + -
55A GLY* 4.8 1.0 - - - -
56A LYS* 3.4 50.3 - - - +
57A ALA* 1.3 78.7 - - - +
59A LYS* 1.3 64.5 + - - +
60A VAL* 3.8 13.9 - - + -
112A ILE 3.4 0.2 - - - +
113A ASP* 3.2 6.2 - - - +
114A ALA 2.9 37.9 + - - +
138A GLU* 3.4 30.1 + - - +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 1.3 72.5 - - - +
60A VAL* 1.3 62.2 + - - +
61A SER* 3.6 0.9 + - - -
111A PRO* 4.2 20.5 + - + +
112A ILE 3.3 5.6 - - - +
113A ASP* 2.8 37.4 + - - +
138A GLU* 2.8 35.2 + - + +
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Residues in contact with VAL 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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6A ILE* 4.7 1.1 - - + -
54A LEU* 4.1 11.0 - - + -
58A ARG* 4.0 20.9 - - + +
59A LYS* 1.3 72.6 - - - +
61A SER* 1.3 58.1 + - - +
62A SER 4.5 2.5 - - - +
63A ILE* 4.5 7.4 - - + -
108A PHE* 3.7 15.4 - - + -
111A PRO* 3.4 1.9 - - - +
112A ILE* 2.7 66.5 + - + +
114A ALA* 4.5 6.5 - - + -
117A ILE* 4.5 3.4 - - + -
136A VAL* 3.7 25.4 - - + -
137A TYR 3.3 12.6 - - - +
138A GLU* 4.6 0.2 - - - +
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Residues in contact with SER 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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3A GLU* 3.3 16.9 + - - +
59A LYS 3.6 1.2 + - - -
60A VAL* 1.3 75.1 - - - +
62A SER* 1.3 59.3 + - - +
107A THR* 3.3 7.2 - - - +
108A PHE* 2.7 43.0 + - - +
111A PRO* 4.4 14.1 - - - -
137A TYR 2.9 4.0 + - - -
138A GLU 3.3 27.1 - - - -
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Residues in contact with SER 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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3A GLU* 2.7 24.7 + - - -
60A VAL* 3.6 1.5 - - - +
61A SER* 1.3 83.1 - - - +
63A ILE* 1.3 72.3 + - - +
105A THR* 5.9 2.5 - - - -
106A VAL 3.1 13.7 - - - -
107A THR* 3.7 14.4 - - - -
108A PHE* 4.3 2.7 - - - -
136A VAL* 3.7 1.6 - - - +
137A TYR* 2.9 44.1 + - - +
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Residues in contact with ILE 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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60A VAL* 4.5 2.5 - - + -
62A SER* 1.3 82.2 - - - +
64A ALA* 1.3 61.3 + - - +
65A ILE* 3.7 24.8 - - + +
81A ILE* 4.3 12.6 - - + -
104A LYS 3.7 1.6 - - - +
105A THR* 3.4 5.6 - - - -
106A VAL* 2.8 37.0 + - + +
108A PHE* 3.7 30.3 - - + -
112A ILE* 5.6 0.9 - - + -
117A ILE* 4.0 30.1 - - + -
119A ILE* 4.9 4.9 - - + -
134A LEU* 4.4 18.2 - - + -
135A ASN 3.4 11.9 - - - +
136A VAL* 4.3 13.9 - - + -
137A TYR* 4.7 1.1 - - - -
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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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63A ILE* 1.3 71.9 - - - +
65A ILE* 1.3 62.1 + - - +
66A THR* 3.8 4.1 + - - +
103A VAL* 3.9 18.2 - - + -
104A LYS 3.6 3.4 - - - -
105A THR* 4.4 8.5 - - + -
133A GLU 3.7 2.1 - - - +
134A LEU* 3.5 6.2 - - - +
135A ASN* 3.1 35.4 + - + +
137A TYR* 4.0 23.4 - - + +
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Residues in contact with ILE 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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63A ILE* 3.7 31.4 - - + +
64A ALA* 1.3 72.4 - - - +
66A THR* 1.3 61.6 + - - +
67A PRO* 3.3 9.7 - - + +
76A ILE* 5.5 0.7 - - + -
81A ILE* 4.8 4.0 - - + -
97A TRP* 3.7 42.8 - - + -
103A VAL* 4.3 1.1 - - - -
104A LYS* 2.8 51.7 + - + +
106A VAL* 4.4 7.2 - - + -
119A ILE* 5.1 5.2 - - + -
131A ILE* 3.9 33.0 - - + -
133A GLU 3.9 2.5 - - - -
134A LEU* 4.5 11.4 - - + +
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Residues in contact with THR 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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32A ILE* 4.4 17.9 - - + +
64A ALA* 4.5 4.5 + - - +
65A ILE* 1.3 72.0 - - - +
67A PRO* 1.3 75.2 - - + +
101A ASN 5.5 1.3 - - - +
103A VAL* 3.8 24.3 - - + +
131A ILE* 3.8 3.5 - - - -
132A ALA* 2.9 26.6 + - + -
133A GLU* 2.9 37.9 + - + +
135A ASN* 4.9 4.0 + - - -
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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