Contacts of the strand formed by residues 40 - 49 (chain A) in PDB entry 2E3V
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 ILE 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PRO* 4.3 15.3 - - + -
31A GLU* 3.1 45.8 - - + +
32A PRO 4.3 4.7 - - - +
34A ALA* 4.5 7.4 - - + +
38A VAL 3.9 1.7 + - - +
39A PRO* 1.3 79.6 - - - +
41A LEU* 1.3 61.9 + - - +
42A LYS 3.5 15.3 - - - +
43A TYR* 3.6 23.8 - - + +
62A ALA* 3.3 17.6 - - + +
88A ALA* 4.0 8.1 - - + -
89A LEU 3.5 11.9 - - - +
90A ASN* 4.2 2.0 - - + -
1004A PEG 3.9 15.0 + - - +
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Residues in contact with LEU 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 PRO* 3.9 27.6 - - + +
40A ILE* 1.3 76.1 - - - +
42A LYS* 1.3 79.4 + - + +
61A ASP* 3.8 3.3 - - - +
62A ALA* 3.0 20.3 + - - +
63A LYS 4.7 0.3 + - - -
89A LEU* 2.7 20.9 + - + +
90A ASN* 3.9 9.2 - - - +
91A GLY* 3.8 23.1 - - - +
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Residues in contact with LYS 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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40A ILE* 3.5 7.3 - - - +
41A LEU* 1.3 96.0 - - + +
43A TYR* 1.3 65.7 + - - +
59A TRP* 3.7 22.9 - - + -
60A TYR 3.3 15.9 - - - +
61A ASP* 2.9 28.8 + - - +
62A ALA 3.9 2.0 - - - +
88A ALA* 3.6 0.7 - - - -
89A LEU* 2.8 46.5 + - + +
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Residues in contact with TYR 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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13A PRO* 4.2 9.4 - - + -
29A PHE* 3.4 34.6 - + + -
31A GLU* 3.7 6.1 - - + +
40A ILE* 3.6 22.8 - - + +
42A LYS* 1.3 74.3 - - - +
44A LYS* 1.3 61.9 + - - +
45A ALA 4.1 0.4 - - - -
59A TRP* 3.4 8.9 - - - -
60A TYR* 2.8 42.8 + - + +
62A ALA* 3.8 33.3 - - + +
65A ALA* 3.9 17.0 - - + -
66A SER* 5.9 0.2 - - - -
71A VAL* 4.6 7.6 - - + -
86A LEU* 5.5 5.8 - - + -
87A ALA 3.2 15.3 - - - +
88A ALA* 3.7 23.1 - - + -
89A LEU 4.8 0.2 - - - +
1004A PEG 3.5 26.5 - - - -
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Residues in contact with LYS 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 TYR* 1.3 75.4 - - - +
45A ALA* 1.3 66.0 + - - +
46A GLU* 4.5 15.3 + - + +
57A SER* 3.7 27.5 + - - -
58A LYS 3.5 9.9 - - - +
59A TRP* 3.5 48.7 - - + +
86A LEU* 3.3 3.4 - - - -
87A ALA* 2.8 43.9 + - + +
94A LEU* 4.4 21.2 - - + +
97A ILE* 4.5 4.6 - - + +
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Residues in contact with ALA 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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43A TYR 4.1 0.8 - - - -
44A LYS* 1.3 74.2 - - - +
46A GLU* 1.3 61.1 + - - +
47A TRP* 4.0 11.9 - - + -
57A SER* 3.0 8.1 - - - -
58A LYS 2.9 29.6 + - - -
60A TYR* 3.6 26.4 - - + +
71A VAL* 4.3 5.2 - - + -
73A ILE* 4.7 6.3 - - + -
85A ARG 3.4 4.9 - - - +
86A LEU* 3.5 21.3 - - + -
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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 LYS* 4.2 19.4 + - + -
45A ALA* 1.3 79.7 - - - +
47A TRP* 1.3 62.7 + - - +
55A TRP* 3.7 20.9 - - + +
56A HIS 3.1 8.7 - - - +
57A SER* 3.9 13.6 - - - -
84A VAL* 3.3 4.4 - - - +
85A ARG* 2.8 74.5 + - + +
97A ILE* 3.4 18.1 - - + +
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Residues in contact with TRP 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 ALA* 3.6 9.2 - - + -
46A GLU* 1.3 83.2 - - - +
48A ARG* 1.3 64.5 + - - +
55A TRP* 3.5 3.7 - - - -
56A HIS* 2.8 64.0 + + + +
57A SER* 3.5 36.3 - - - -
58A LYS* 3.5 22.7 - - + -
60A TYR* 4.6 0.2 - - - -
73A ILE* 3.4 44.0 - - + -
74A VAL 4.5 8.7 + - - -
76A LEU* 3.6 28.2 - - + +
82A TYR* 4.0 15.5 - + + -
83A ALA 3.1 13.5 - - - +
84A VAL* 4.3 2.7 - - + -
103A PHE* 5.2 1.1 - - + -
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Residues in contact with ARG 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 TRP* 1.3 79.6 - - - +
49A ALA* 1.3 67.5 + - - +
52A GLU* 3.4 29.5 + - + -
53A GLU* 2.9 40.7 + - - +
54A VAL 3.3 21.5 - - - +
55A TRP* 3.2 44.3 - - + +
56A HIS* 5.3 2.7 - - - -
82A TYR* 3.7 5.6 - - - -
83A ALA* 2.8 38.6 + - - +
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Residues in contact with ALA 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 ARG* 1.3 82.3 + - - +
50A VAL* 1.3 71.8 + - - +
51A GLY 3.2 0.2 + - - -
52A GLU* 3.0 34.3 + - + +
56A HIS* 5.8 1.4 - - - -
77A LYS* 6.1 2.7 - - + -
80A THR* 3.8 16.2 - - + -
81A THR 3.3 6.5 - - - -
82A TYR* 3.5 24.9 - - + +
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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