Contacts of the strand formed by residues 50 - 56 (chain A) in PDB entry 5I2C
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 ASP 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A SER* 2.4 31.6 + - - +
15A VAL 3.3 11.2 - - - +
16A ALA* 4.2 2.0 - - - -
17A ARG* 3.9 4.6 - - - +
45A THR 3.8 0.2 - - - +
46A GLU* 3.7 2.1 - - - +
47A THR* 2.6 61.6 + - - +
48A PRO 3.6 1.0 - - - -
49A GLU* 1.3 92.1 - - + +
51A TYR* 1.3 67.2 + - - +
52A THR* 2.8 28.6 + - - -
300A THR* 5.0 1.2 + - - -
301A PHE* 3.7 3.7 - - - +
302A ASN* 4.2 6.5 + - - +
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Residues in contact with TYR 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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14A SER* 3.4 0.9 - - - -
15A VAL* 2.8 51.7 + - + +
17A ARG* 3.1 38.8 + - - -
20A LEU* 3.5 38.0 - - + +
27A LEU* 5.2 1.8 - - + -
44A LEU* 3.6 24.5 - - + -
45A THR 3.4 4.9 - - - -
46A GLU* 3.2 29.8 + - + -
50A ASP* 1.3 74.8 - - - +
52A THR* 1.3 62.5 + - - +
53A LEU* 3.7 5.3 + - + +
205A LEU* 2.6 33.2 + - + -
206A PHE* 3.9 20.1 - + - -
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Residues in contact with THR 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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12A VAL* 4.7 7.6 - - + -
13A LEU 3.4 11.7 - - - +
43A SER 3.5 1.0 - - - +
44A LEU* 3.4 4.9 - - - -
45A THR* 2.8 45.1 + - - -
50A ASP* 2.8 21.2 + - - -
51A TYR* 1.3 72.2 - - - +
53A LEU* 1.3 70.6 + - - +
54A MET* 4.9 6.7 - - + -
299A SER 4.8 3.6 - - - +
300A THR* 3.4 21.4 - - + -
301A PHE* 2.9 32.3 + - + +
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Residues in contact with LEU 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 ARG 3.7 0.9 - - - +
12A VAL* 3.5 3.3 - - - -
13A LEU* 2.8 51.7 + - + +
15A VAL* 4.1 15.5 - - + -
27A LEU* 3.7 21.1 - - + -
42A PHE* 4.4 7.2 - - + -
43A SER 3.2 4.9 - - - +
44A LEU* 3.3 36.3 - - + -
51A TYR* 4.1 10.3 - - + +
52A THR* 1.3 75.7 - - - +
54A MET* 1.3 65.1 + - - +
55A VAL* 4.0 5.4 - - + -
63A LEU* 3.9 37.2 - - + -
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Residues in contact with MET 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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10A VAL* 4.0 11.9 - - + -
11A ARG 3.4 4.0 - - - -
12A VAL* 4.1 19.1 - - + -
41A PHE* 3.7 13.0 - - + -
42A PHE* 3.6 2.4 - - - -
43A SER* 2.9 39.2 + - - +
52A THR* 4.9 7.4 - - + +
53A LEU* 1.3 76.2 - - - +
55A VAL* 1.3 60.1 + - - +
113A LEU* 4.4 23.6 - - + -
114A MET 4.3 12.1 - - - +
115A LEU* 4.4 26.9 - - + -
124A LEU* 3.9 19.1 - - - -
299A SER* 3.4 28.0 - - - +
300A THR 5.8 0.4 - - - -
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Residues in contact with VAL 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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10A VAL* 3.9 5.3 - - - +
11A ARG* 2.8 31.0 + - - +
13A LEU* 3.7 26.0 - - + -
30A LEU* 4.3 4.7 - - + -
39A CYS* 3.7 7.4 - - - -
41A PHE 3.3 11.0 - - - +
42A PHE* 4.1 17.5 - - + -
53A LEU* 5.0 2.9 - - + -
54A MET* 1.3 74.7 - - - +
56A ASP* 1.3 69.1 + - - +
59A GLY* 3.4 27.6 - - - +
60A PHE* 3.7 23.6 - - + +
63A LEU* 4.2 6.7 - - + -
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Residues in contact with ASP 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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8A HIS* 4.9 3.3 + - + +
9A ARG 3.2 20.6 - - - +
10A VAL* 4.2 2.5 - - + +
11A ARG 4.9 0.4 - - - -
38A ARG 4.2 2.4 - - - +
39A CYS* 3.3 13.2 - - - -
40A LYS* 2.9 38.5 + - - +
41A PHE* 3.1 25.5 + - + +
55A VAL* 1.3 75.9 - - - +
57A GLU* 1.3 63.9 + - - +
58A GLU* 3.3 7.2 + - - +
59A GLY 3.0 19.2 + - - -
60A PHE* 2.9 19.5 + - - +
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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