Contacts of the strand formed by residues 38 - 51 (chain A) in PDB entry 2P80
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 VAL 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 5.9 1.3 - - + -
12A LEU* 4.8 1.7 - - + +
13A PRO 3.1 6.1 + - - -
14A ARG* 3.0 57.7 - - + +
15A GLN 3.0 24.7 + - - -
37A LYS* 1.3 68.9 - - - +
39A VAL* 1.3 60.4 + - - +
40A GLU* 3.6 11.3 + - + -
80A TYR* 3.3 31.9 - - + +
82A GLU* 3.9 22.2 - - + +
123A ARG* 4.5 12.3 - - - +
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Residues in contact with VAL 39 (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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15A GLN* 3.5 18.6 - - - +
17A VAL* 4.1 8.3 - - + -
37A LYS* 3.3 17.9 - - + +
38A VAL* 1.3 72.3 - - - +
40A GLU* 1.3 61.8 + - - +
41A PHE* 2.7 42.1 - - + -
74A VAL 5.0 1.3 - - - +
75A VAL* 3.5 29.2 - - + -
79A ASP* 4.1 6.7 - - + +
80A TYR 2.8 9.2 + - - +
81A LEU* 3.7 1.4 - - - -
82A GLU* 2.8 27.4 + - - +
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Residues in contact with GLU 40 (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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14A ARG* 3.4 32.9 - - - +
15A GLN 2.9 9.9 + - - +
16A LYS* 3.1 50.2 + - + +
17A VAL 3.1 24.9 + - - +
38A VAL* 3.9 13.7 - - + +
39A VAL* 1.3 79.1 - - - +
41A PHE* 1.3 64.7 + - - +
82A GLU* 3.3 23.7 - - + +
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Residues in contact with PHE 41 (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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17A VAL* 2.8 51.8 - - + -
19A LEU* 3.5 35.2 - - + -
26A HIS* 5.0 4.5 - + - -
39A VAL* 2.7 47.1 - - + -
40A GLU* 1.3 78.4 - - - +
42A THR* 1.3 62.1 + - - +
73A MET* 4.0 18.2 - - + -
74A VAL 4.6 14.1 - - - -
75A VAL* 4.2 8.5 - - + -
81A LEU* 4.3 13.0 - - + -
82A GLU 3.0 7.0 + - - +
83A LEU* 3.0 11.3 - - + +
84A THR 3.0 22.0 + - - -
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Residues in contact with THR 42 (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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17A VAL 5.2 1.2 + - - -
19A LEU* 4.4 6.3 - - - +
41A PHE* 1.3 73.7 - - - +
43A MET* 1.3 71.2 + - - +
44A VAL* 5.0 3.1 - - + -
65A ASN* 4.0 4.9 - - - +
84A THR* 3.2 32.1 - - + +
86A ILE* 3.8 23.8 - - + -
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Residues in contact with MET 43 (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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19A LEU* 3.9 10.1 - - + -
42A THR* 1.3 82.1 - - - +
44A VAL* 1.3 62.4 + - - +
64A PHE* 4.4 15.7 - - + -
65A ASN* 3.5 22.4 - - - +
71A PRO* 3.3 38.8 - - + -
73A MET* 3.5 29.4 - - + -
83A LEU* 3.8 26.5 - - + +
84A THR 3.1 8.0 + - - -
85A LEU* 3.0 29.0 - - + +
86A ILE 3.2 9.9 + - - -
97A ILE* 4.5 9.2 - - + -
134A TYR* 5.1 2.7 - - + -
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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
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42A THR* 5.0 3.8 - - + -
43A MET* 1.3 75.0 - - - +
45A ILE* 1.3 68.2 + - - +
46A GLU* 3.8 14.3 + - + +
65A ASN* 2.9 26.7 + - - +
66A GLY 3.8 1.9 + - - -
86A ILE* 3.4 30.7 - - + +
88A PRO* 3.4 33.4 - - + -
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Residues in contact with ILE 45 (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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44A VAL* 1.3 73.5 - - - +
46A GLU* 1.3 70.6 + - - +
47A GLU* 4.7 1.3 - - + -
63A ALA 3.3 17.3 - - - +
64A PHE* 2.8 41.1 - - + -
85A LEU* 3.2 26.5 - - + -
86A ILE 3.0 11.6 + - - +
87A ASN* 4.3 2.7 - - + +
88A PRO* 3.3 10.9 - - - +
91A ASN* 3.0 23.9 + - - +
95A HIS* 4.0 27.1 - - + +
114A ILE* 4.4 5.6 - - + -
150A MET* 3.5 22.7 - - + -
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Residues in contact with GLU 46 (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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44A VAL* 4.2 18.2 - - + +
45A ILE* 1.3 81.1 - - - +
47A GLU* 1.3 65.0 + - - +
48A LYS* 3.5 27.8 + - + +
61A ALA 3.6 1.0 - - - +
63A ALA* 2.9 31.6 + - - +
65A ASN 4.8 2.1 - - - +
66A GLY* 3.6 28.3 + - - -
88A PRO* 5.4 2.5 - - + -
91A ASN* 4.3 2.2 - - - +
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Residues in contact with GLU 47 (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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45A ILE* 4.7 1.8 - - + -
46A GLU* 1.3 74.8 - - - +
48A LYS* 1.3 60.2 + - - +
60A HIS* 6.2 1.1 - - - -
61A ALA 3.2 7.9 - - - +
62A MET* 4.4 12.8 - - + -
91A ASN* 3.5 27.2 + - - +
92A THR* 3.2 23.3 + - - +
93A LEU* 3.3 25.8 + - - +
95A HIS* 2.1 46.3 + - + +
199A PRO* 4.7 9.4 - - + +
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Residues in contact with LYS 48 (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 GLU* 3.8 28.6 + - + +
47A GLU* 1.3 76.6 - - - +
49A LYS* 1.3 66.5 + - - +
50A ILE* 3.8 22.1 + - + -
60A HIS* 3.5 4.0 - - - -
61A ALA* 2.8 33.0 + - + +
63A ALA* 5.6 2.9 - - - -
66A GLY* 3.7 26.3 + - - -
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Residues in contact with LYS 49 (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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48A LYS* 1.3 78.0 - - - +
50A ILE* 1.3 63.9 + - - +
58A GLU* 4.7 25.4 + - + +
59A VAL 4.0 4.3 - - - -
60A HIS* 3.1 49.6 - - + +
196A TYR 4.2 12.4 + - - +
197A GLU* 4.5 8.3 + - - +
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Residues in contact with ILE 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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48A LYS* 4.0 30.1 - - + -
49A LYS* 1.3 78.8 - - - +
51A VAL* 1.3 66.4 + - - +
52A ILE* 3.6 19.5 - - + +
58A GLU* 3.4 2.8 - - - -
59A VAL* 3.0 36.8 + - + +
61A ALA* 3.8 19.7 - - + -
68A VAL* 4.9 10.8 - - + -
183A PHE* 5.4 5.6 - - + -
222A GLY* 4.1 14.6 - - - +
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Residues in contact with VAL 51 (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 LYS 5.9 0.2 - - - +
50A ILE* 1.3 75.6 - - - +
52A ILE* 1.3 71.8 + - - +
53A ASP 3.5 22.9 - - - +
56A GLY* 3.8 13.2 - - - +
57A THR 3.1 15.7 - - - +
58A GLU* 4.1 17.9 - - + +
222A GLY 4.2 0.9 - - - +
223A ALA* 4.1 9.5 - - - +
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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