Contacts of the strand formed by residues 38 - 55 (chain A) in PDB entry 2DT4
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 ALA 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ILE* 4.0 7.6 - - + -
37A THR* 1.3 78.4 - - - +
39A ILE* 1.3 66.6 - - - +
78A ASN* 3.3 8.1 - - - +
79A VAL* 2.8 40.4 + - + +
118A LEU* 3.6 29.2 - - + -
119A GLN 3.1 15.5 - - - +
120A GLU* 4.0 0.7 - - - -
121A LEU* 4.2 4.7 - - - +
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Residues in contact with ILE 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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38A ALA* 1.3 80.6 - - - +
40A ILE* 1.3 67.9 + - - +
41A ASN* 5.8 2.5 - - + +
77A GLY 3.6 9.4 - - - +
78A ASN* 4.6 6.3 - - + -
117A PHE* 4.1 17.3 - - + -
118A LEU* 3.3 4.9 - - - +
119A GLN* 2.9 58.5 + - + +
121A LEU* 4.3 18.8 - - + -
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Residues in contact with ILE 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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26A ILE* 4.2 14.1 - - + -
39A ILE* 1.3 86.4 - - - +
41A ASN* 1.3 65.6 + - - +
75A LEU* 3.9 19.3 - - + -
76A ILE* 3.5 4.9 - - - +
77A GLY* 3.0 46.0 + - - +
78A ASN 3.7 10.1 - - - +
79A VAL* 4.5 8.1 - - + -
88A VAL* 3.8 29.2 - - + -
90A ALA* 4.4 4.0 - - + -
116A ILE* 4.6 7.4 - - + -
117A PHE 3.2 8.1 - - - +
118A LEU* 3.7 29.4 - - + -
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Residues in contact with ASN 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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39A ILE* 5.8 2.0 - - + +
40A ILE* 1.3 77.7 - - - +
42A GLY* 1.3 62.9 + - - +
75A LEU* 3.1 16.6 - - - +
76A ILE* 4.8 7.6 - - + -
116A ILE* 3.6 3.7 - - - +
117A PHE* 2.8 59.7 + - - +
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Residues in contact with GLY 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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41A ASN* 1.3 81.6 + - - +
43A ILE* 1.3 71.4 + - - +
72A LEU* 4.6 1.8 - - - -
74A SER* 3.7 2.4 - - - -
75A LEU* 2.9 38.2 + - - +
115A GLU 3.2 13.0 - - - -
116A ILE* 4.1 8.1 - - - -
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Residues in contact with ILE 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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42A GLY* 1.3 81.2 - - - +
44A GLY* 1.3 60.7 + - - +
72A LEU* 3.4 18.3 - - - +
73A ILE* 3.5 20.6 - - - +
74A SER* 5.0 0.2 - - - -
114A ALA* 3.4 3.5 - - - -
115A GLU* 2.8 54.5 + - + +
116A ILE* 4.8 0.4 - - - +
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Residues in contact with GLY 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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43A ILE* 1.3 80.8 - - - +
45A THR* 1.3 61.2 + - - -
71A GLU* 3.5 9.8 - - - +
72A LEU* 2.8 32.7 + - - +
113A VAL* 3.2 20.2 - - - -
114A ALA* 4.4 0.2 - - - -
115A GLU* 5.8 1.1 - - - -
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Residues in contact with THR 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 GLY* 1.3 73.7 + - - -
46A LEU* 1.3 75.9 + - - +
69A SER* 4.1 18.2 - - - -
70A TYR 3.3 14.1 + - - +
71A GLU* 3.4 24.4 + - - +
72A LEU* 3.8 1.5 - - - +
112A PHE* 2.8 55.3 + - + -
113A VAL* 2.8 16.6 + - - +
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Residues in contact with LEU 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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22A LEU* 4.2 24.5 - - + -
45A THR* 1.3 81.6 - - - +
47A LYS* 1.3 64.2 + - - +
49A PRO* 4.1 20.6 - - + +
68A GLY 3.7 0.9 - - - +
69A SER* 3.4 2.3 - - - -
70A TYR* 2.9 33.4 + - - +
72A LEU* 4.0 28.4 - - + +
94A LEU* 4.2 14.4 - - + -
106A LEU* 4.2 24.9 - - + -
109A GLY* 4.3 7.9 - - - +
110A GLU 3.2 15.9 - - - +
111A VAL* 4.0 14.4 - - + -
113A VAL 5.1 1.8 - - - +
114A ALA* 5.2 0.7 - - + -
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Residues in contact with LYS 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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18A GLU* 4.7 5.5 + - - -
46A LEU* 1.3 74.5 - - - +
48A ASN* 1.3 82.7 + - - +
49A PRO 3.3 1.9 - - - -
68A GLY* 3.4 5.2 - - - +
69A SER* 3.4 28.5 - - - +
110A GLU* 2.8 54.2 + - + +
112A PHE* 3.8 42.7 - - + +
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Residues in contact with ASN 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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47A LYS* 1.3 82.7 + - - +
49A PRO* 1.3 69.2 - - - +
50A LYS* 3.6 12.5 + - - +
66A LEU 3.3 15.7 - - - +
67A LYS* 3.6 10.5 - - + +
68A GLY* 2.9 38.3 + - - -
108A GLU* 4.5 3.8 - - - +
109A GLY* 4.8 1.6 - - - -
110A GLU* 4.8 8.7 + - - -
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Residues in contact with PRO 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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46A LEU* 4.1 24.0 - - + +
47A LYS* 3.3 8.5 - - - +
48A ASN* 1.3 90.4 - - - +
50A LYS* 1.3 59.5 + - - +
66A LEU* 2.9 36.6 + - + +
68A GLY 3.9 8.3 - - - +
70A TYR* 4.1 22.7 - - + -
94A LEU* 3.7 30.5 - - + -
106A LEU* 4.8 3.6 - - + -
108A GLU 3.5 10.3 - - - +
109A GLY* 4.2 2.0 - - - -
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Residues in contact with LYS 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 ASN* 4.2 7.2 + - - +
49A PRO* 1.3 76.1 - - - +
51A ILE* 1.3 62.3 + - - +
63A VAL* 4.1 20.6 - - + -
64A ILE 3.5 4.0 - - - -
65A PRO* 4.1 22.7 - - + -
66A LEU 5.7 0.2 - - - +
106A LEU* 3.7 5.2 - - - +
107A VAL* 2.9 34.1 + - + -
108A GLU* 2.8 58.2 + - + +
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Residues in contact with ILE 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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50A LYS* 1.3 77.6 - - - +
52A GLY* 1.3 57.4 + - - +
63A VAL* 3.4 4.7 - - - +
64A ILE* 2.8 62.5 + - + +
66A LEU* 4.1 17.5 - - + -
92A VAL* 3.8 17.9 - - + -
94A LEU* 3.7 26.7 - - + -
102A PHE* 4.4 4.9 - - + -
103A GLY 3.6 33.2 - - - +
104A GLY 4.2 9.0 - - - +
105A HIS 3.2 8.1 - - - +
106A LEU* 4.9 1.1 - - + -
107A VAL* 3.8 4.7 - - - -
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Residues in contact with GLY 52 (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* 1.3 76.1 - - - +
53A TYR* 1.3 60.6 + - - +
61A TYR* 3.8 16.1 - - - -
62A LYS 3.2 9.2 - - - -
64A ILE* 5.8 1.3 - - - -
104A GLY* 3.7 6.6 - - - -
105A HIS* 2.7 38.2 + - - +
107A VAL* 3.7 9.9 - - - +
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLY* 1.3 71.5 - - - -
54A PHE* 1.3 77.4 + - - +
55A LEU* 3.5 20.7 + - + -
61A TYR* 3.7 1.8 - - - -
62A LYS* 2.8 47.4 + - + +
64A ILE* 5.1 10.4 - - + +
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Residues in contact with PHE 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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53A TYR* 1.3 90.2 - - - +
55A LEU* 1.3 60.9 + - - +
56A GLU* 3.8 29.1 + - + +
59A LYS* 3.7 14.4 - - - -
60A GLU* 3.5 29.2 - - - -
61A TYR* 3.5 22.9 - + + -
133A TYR* 3.4 27.6 - - + -
134A GLY 4.2 4.9 - - - -
135A LEU* 3.4 37.7 - - + -
1144A GOL 3.1 31.8 + - - +
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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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53A TYR* 3.9 31.0 - - + +
54A PHE* 1.3 71.9 - - - +
56A GLU* 1.3 59.7 + - - +
57A GLU* 3.3 2.7 - - + +
58A LYS* 3.1 42.5 + - + +
59A LYS* 2.8 25.3 + - - -
60A GLU* 2.9 23.1 + - + +
61A TYR 5.0 0.7 - - - -
62A LYS* 4.0 28.3 - - + +
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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