Contacts of the strand formed by residues 3 - 9 (chain D) in PDB entry 5YL4
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 3 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ARG* 1.3 98.5 - - - +
4D ILE* 1.3 59.9 - - - +
48D ASN* 3.5 19.9 - - - +
49D VAL 3.7 5.2 - - - -
62D ARG* 3.5 18.2 - - - +
126D SER 5.1 0.3 - - - +
127D CYS* 3.4 25.8 - - + +
128D ASP* 3.2 23.2 + - - +
129D CYS 2.8 36.2 + - - +
130D LEU* 3.5 5.1 - - - +
131D GLN* 2.9 29.6 + - - +
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Residues in contact with ILE 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLU* 1.3 73.5 - - - +
5D VAL* 1.3 67.0 + - - +
6D HIS 3.9 2.0 + - - -
49D VAL* 2.8 41.7 + - + +
50D TYR* 3.7 26.1 - - + +
62D ARG* 3.3 17.7 + - - +
131D GLN* 3.5 26.7 - - + +
132D GLY 3.5 12.1 - - - +
134D GLN* 3.9 31.9 - - + +
240D LEU* 3.8 20.4 - - + -
250D LEU* 3.8 17.5 - - + -
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Residues in contact with VAL 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 1.3 73.4 - - - +
6D HIS* 1.3 64.3 + - - +
7D ILE* 3.8 3.5 + - + +
62D ARG* 3.7 26.7 - - + +
64D ILE* 3.7 29.8 - - + -
120D VAL* 4.9 2.2 - - + -
123D GLU* 4.5 6.1 - - + -
124D SER* 4.0 17.3 - - - +
127D CYS* 4.4 3.8 - - - -
130D LEU* 3.6 22.2 - - + -
132D GLY 3.0 7.7 + - - -
133D PHE* 3.4 27.4 - - + +
134D GLN 3.2 20.6 + - - -
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Residues in contact with HIS 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.9 3.0 + - - +
5D VAL* 1.3 74.6 - - - +
7D ILE* 1.3 70.1 + - - +
8D GLN* 3.0 32.7 + - + +
17D GLY* 4.2 3.6 - - - -
20D PHE* 4.3 11.0 - + - -
21D TRP* 3.2 36.4 + - + -
50D TYR* 5.1 3.4 - - + -
62D ARG 3.0 16.1 + - - +
63D ALA* 3.5 9.9 - - + -
64D ILE* 3.1 22.3 + - - +
134D GLN* 3.4 33.9 + - + +
136D THR* 3.7 30.0 + - + -
233D MET* 5.0 0.2 - - + -
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Residues in contact with ILE 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 4.4 5.2 - - + +
6D HIS* 1.3 84.2 + - - +
8D GLN* 1.3 66.5 + - - +
9D ALA* 4.8 0.4 - - + +
64D ILE* 3.6 24.5 - - + +
66D VAL* 4.5 12.1 - - + -
116D VAL* 5.5 0.2 - - + -
120D VAL* 4.2 14.1 - - + -
133D PHE* 4.6 12.8 - - + -
134D GLN 2.8 10.4 + - - +
135D LEU* 3.2 24.9 - - + +
136D THR* 2.8 26.5 + - - -
151D LEU* 4.6 15.0 - - + -
155D ILE* 3.5 33.4 - - + -
164D MET* 6.3 0.4 - - - -
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Residues in contact with GLN 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D HIS* 3.0 26.8 + - + +
7D ILE* 1.3 72.6 - - - +
9D ALA* 1.3 59.4 + - - +
13D GLY 3.4 10.5 - - - +
14D ASN* 2.8 44.1 + - - +
17D GLY* 3.4 14.6 - - - -
18D ALA* 4.4 2.4 - - - +
21D TRP* 3.8 6.9 + - - -
64D ILE 3.1 12.3 + - - +
65D LEU* 3.4 27.2 - - + +
66D VAL* 2.9 30.1 + - - +
76D VAL* 4.5 4.8 - - - +
85D PHE* 5.1 1.9 - - - -
136D THR* 3.1 20.6 - - - +
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Residues in contact with ALA 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 5.1 0.4 - - + -
8D GLN* 1.3 72.3 - - - +
10D GLY* 1.3 65.3 + - - +
13D GLY* 3.6 12.9 + - - -
66D VAL* 3.4 19.5 - - + +
135D LEU* 4.1 17.2 - - + +
136D THR 3.1 10.0 + - - +
137D HIS* 3.8 2.6 - - + +
138D SER 4.8 0.5 + - - -
143D THR* 5.0 3.1 - - + +
144D GLY* 3.4 27.1 - - - +
147D MET* 5.9 0.4 - - + -
148D GLY* 4.4 11.7 - - - +
151D LEU* 4.8 4.7 - - + -
501D GTP 4.6 0.3 + - - -
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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