Contacts of the strand formed by residues 41 - 52 (chain A) in PDB entry 5ITY
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 GLU 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLY* 3.4 20.6 - - - +
26A CYS* 3.7 21.9 - - - -
40A PHE* 1.3 75.8 - - - +
42A SER* 1.3 65.4 + - - +
68A PRO* 3.8 33.3 - - + +
70A GLN* 3.0 26.8 + - - +
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Residues in contact with SER 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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24A GLY* 3.2 5.0 - - - -
25A GLY* 2.7 36.6 + - - +
40A PHE* 3.8 23.9 - - - -
41A GLU* 1.3 78.8 - - - +
43A SER* 1.3 61.5 + - - +
44A ALA 3.3 15.1 + - - -
45A TYR* 3.6 8.0 - - - -
62A PRO* 3.9 5.6 - - - +
66A ALA* 3.5 16.3 - - - +
67A GLN 3.8 7.9 - - - -
68A PRO* 4.4 1.2 + - - -
70A GLN* 4.3 6.7 - - - -
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Residues in contact with SER 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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23A PHE 3.8 0.5 - - - +
24A GLY* 3.7 11.7 - - - -
25A GLY 4.4 4.3 - - - +
42A SER* 1.3 73.2 + - - +
44A ALA* 1.3 64.2 + - - +
66A ALA* 3.6 5.7 - - - -
67A GLN* 2.8 38.7 + - - +
68A PRO* 4.8 0.2 - - - +
104A ALA* 4.3 8.3 - - - +
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Residues in contact with ALA 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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22A VAL* 3.9 16.2 - - + -
23A PHE 3.2 5.8 - - - -
42A SER* 3.2 4.2 + - - -
43A SER* 1.3 88.3 + - - +
45A TYR* 1.3 53.3 + - - +
62A PRO* 3.3 4.5 - - - +
63A LEU* 2.7 46.9 + - + -
66A ALA* 3.6 7.9 - - + +
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Residues in contact with TYR 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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22A VAL* 3.6 4.3 - - - +
23A PHE* 2.6 80.5 + - + +
24A GLY* 3.5 12.5 + - - -
25A GLY 4.2 4.0 - - - -
26A CYS 4.2 5.4 + - - -
27A VAL* 4.1 6.8 - - - +
40A PHE* 3.8 29.8 - + + -
42A SER* 3.6 18.2 - - - +
44A ALA* 1.3 74.2 - - - +
46A ARG* 1.3 72.6 + - - +
47A ILE* 3.8 17.0 - - + -
60A LEU* 4.0 15.7 - - + -
61A SER 3.4 18.6 - - - -
62A PRO* 3.6 5.4 - - + -
63A LEU* 4.1 2.7 - - - +
101A PHE* 3.6 26.4 - + - +
102A TYR 4.3 1.7 + - - -
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Residues in contact with ARG 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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19A ARG 4.4 11.9 + - - -
20A ALA* 5.1 3.2 - - - +
21A LEU 4.0 23.1 + - - +
22A VAL* 4.0 12.0 - - + +
45A TYR* 1.3 75.8 - - - +
47A ILE* 1.3 62.9 + - - +
59A ILE 3.5 1.9 - - - +
60A LEU* 3.6 1.9 - - - -
61A SER* 2.8 40.7 + - - +
63A LEU* 3.5 40.1 - - + +
150B ARG* 3.8 38.1 + - - +
151B ASN* 5.6 5.5 + - - -
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Residues in contact with ILE 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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14A VAL* 3.7 11.5 - - + +
18A CYS* 3.6 11.5 + - - +
23A PHE* 3.4 46.7 - - + -
45A TYR* 3.8 9.2 - - + -
46A ARG* 1.3 76.5 - - - +
48A SER* 1.3 58.7 + - - +
58A LEU* 3.7 33.9 - - + -
59A ILE 3.4 5.2 - - - +
60A LEU* 3.5 16.6 - - + -
101A PHE* 3.7 26.0 - - + -
112A LEU* 4.0 8.5 - - + -
150B ARG* 2.5 34.5 + - - +
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Residues in contact with SER 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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14A VAL* 4.3 4.3 - - - -
15A ASN* 3.1 13.2 - - - -
47A ILE* 1.3 76.1 - - - +
49A ALA* 1.3 66.5 + - - +
58A LEU* 3.4 5.5 - - - +
59A ILE* 2.8 37.8 + - - +
61A SER* 5.4 1.4 + - - -
143B GLN* 2.8 31.4 + - - -
146B GLU* 4.6 4.5 - - - -
150B ARG* 3.9 12.1 - - - -
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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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11A SER* 3.8 27.4 - - - +
14A VAL* 4.0 9.0 - - + -
15A ASN* 2.6 29.8 + - - -
48A SER* 1.3 79.2 - - - +
50A SER* 1.3 64.7 + - - +
56A LEU* 4.5 3.8 - - + -
57A ARG 3.1 11.9 - - - +
58A LEU* 3.9 14.1 - - + -
142B GLN* 3.8 4.5 - - - +
143B GLN* 3.2 12.7 + - - +
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Residues in contact with SER 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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11A SER* 3.8 5.8 - - - -
49A ALA* 1.3 77.6 - - - +
51A ALA* 1.3 59.0 + - - +
56A LEU* 3.4 3.8 - - - +
57A ARG* 2.7 44.2 + - - +
59A ILE* 6.1 0.3 - - - +
129A TRP* 4.0 16.9 - - - -
142B GLN* 3.3 26.5 - - - -
143B GLN* 3.8 13.7 + - - +
501B GOL 4.8 5.5 + - - -
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Residues in contact with ALA 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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7A LEU* 3.8 9.4 - - + +
8A HIS* 3.6 37.9 - - + +
11A SER* 3.7 7.4 - - - +
50A SER* 1.3 74.2 - - - +
52A ARG* 1.3 60.9 + - - +
53A GLY 4.2 1.8 - - - +
55A GLU 3.3 11.0 - - - +
56A LEU* 4.2 1.6 - - - +
129A TRP* 4.1 2.0 - - - -
136A CYS* 5.1 0.8 - - - -
139A GLN* 3.0 20.0 - - - +
142B GLN* 2.8 8.8 + - - +
501B GOL 3.3 11.4 + - - -
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Residues in contact with ARG 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 ALA* 1.3 75.4 - - - +
53A GLY* 1.3 69.2 + - - +
54A LYS 3.1 0.5 + - - -
55A GLU* 2.8 28.5 + - - +
129A TRP* 3.6 64.1 - - + +
130A GLN 5.0 0.4 + - - -
133A ARG* 3.6 19.6 + - - +
134A GLY 3.2 30.9 + - - -
135A PRO* 3.7 6.5 - - - +
136A CYS* 3.8 9.4 - - + -
140A GLU* 2.9 30.9 + - - +
172A ASN* 3.6 13.4 + - - +
501B GOL 4.2 8.1 - - - +
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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