Contacts of the strand formed by residues 44 - 51 (chain A) in PDB entry 1C7Y
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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ARG* 3.3 35.6 + - - -
7A GLY* 3.1 20.9 - - - +
8A ILE* 3.6 13.3 - - + +
39A PRO* 3.7 11.8 - - - +
43A GLN* 1.3 77.4 + - - +
45A ALA* 1.3 65.7 + - - +
46A ILE* 4.1 14.4 - - - +
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Residues in contact with ALA 45 (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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5A LEU 3.6 1.4 - - - +
6A ARG* 3.1 5.2 - - - +
7A GLY 2.6 35.2 + - - +
9A ILE* 3.8 31.2 - - + -
19A ILE* 4.6 6.9 - - + +
38A LEU* 4.8 1.1 - - + -
39A PRO* 4.1 13.2 - - + -
43A GLN 3.8 0.2 + - - -
44A GLU* 1.3 75.8 - - - +
46A ILE* 1.3 68.1 + - - +
47A VAL* 4.2 13.0 - - + -
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Residues in contact with ILE 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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4A ARG* 3.5 45.3 - - + +
5A LEU 3.2 4.0 - - - +
6A ARG* 3.3 26.2 - - + -
44A GLU* 4.1 10.8 - - - +
45A ALA* 1.3 80.3 - - - +
47A VAL* 1.3 68.9 + - - +
48A PHE* 5.4 8.0 - - + -
63A PHE 4.7 0.2 - - - +
64A ASN* 4.7 11.4 - - - +
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Residues in contact with VAL 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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4A ARG* 4.3 3.1 - - - -
5A LEU* 2.9 32.7 + - + +
19A ILE* 3.7 29.8 - - + -
28A VAL* 4.5 10.1 - - + -
30A MET* 4.4 5.2 - - - -
38A LEU* 4.0 27.4 - - + -
45A ALA* 4.5 0.9 - - + -
46A ILE* 1.3 85.2 - - - +
48A PHE* 1.3 65.7 + - - +
49A THR* 3.0 21.7 - - + +
62A GLY* 4.9 1.1 - - - -
63A PHE 3.6 12.8 - - - +
64A ASN* 4.4 8.1 - - - +
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Residues in contact with PHE 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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3A GLY 3.5 7.6 - - - -
4A ARG* 4.2 28.0 - - + +
46A ILE* 5.4 7.6 - - + -
47A VAL* 1.3 73.7 - - - +
49A THR* 1.3 59.7 + - - +
62A GLY* 3.1 2.6 - - - -
63A PHE* 2.8 37.9 + - - +
64A ASN 3.7 21.5 - - - -
65A ASN* 3.8 2.2 - - - +
66A LYS* 3.7 45.8 - - + -
69A ARG* 3.6 40.6 - - + +
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Residues in contact with THR 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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2A ILE* 3.3 32.7 + - - +
3A GLY* 3.0 12.6 + - - +
4A ARG 3.6 1.7 + - - -
5A LEU* 4.2 20.6 - - + +
28A VAL* 4.8 2.0 - - + -
47A VAL* 3.0 31.9 - - + +
48A PHE* 1.3 75.6 - - - +
50A HIS* 1.3 59.3 + - - +
51A PHE 3.9 0.2 - - - -
60A LEU* 4.1 16.0 - - + +
61A TYR 3.0 9.6 - - - +
62A GLY* 4.4 2.7 - - - -
69A ARG* 2.6 25.5 + - - +
73A LYS* 5.2 1.4 + - - -
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Residues in contact with HIS 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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49A THR* 1.3 72.7 - - - +
51A PHE* 1.3 69.2 + - - +
52A VAL* 3.7 27.4 + - + +
59A LEU 4.0 0.2 - - - +
60A LEU* 4.5 1.1 - - - -
61A TYR* 2.6 38.8 + + + +
63A PHE* 4.2 7.2 - - + -
69A ARG* 4.6 1.8 - - + -
72A PHE* 3.7 33.2 - + + -
73A LYS* 2.9 36.5 - - + +
76A ILE* 3.4 25.3 - - + +
83A PRO* 5.7 0.9 - - + +
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Residues in contact with PHE 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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1A MET* 4.1 37.0 + - + +
2A ILE* 4.0 31.9 + - + +
49A THR 3.9 2.0 + - - -
50A HIS* 1.3 83.1 + - - +
52A VAL* 1.3 79.1 + - - +
53A VAL* 3.4 28.5 + - + +
58A GLN* 4.0 34.3 - - + -
59A LEU 3.5 2.7 - - - -
60A LEU* 3.3 27.6 - - + -
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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