Contacts of the strand formed by residues 3 - 9 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ARG* 1.3 104.7 + - + +
4B ILE* 1.3 59.3 + - - +
48B ASN* 3.6 12.6 + - - +
49B VAL 3.8 4.7 - - - -
62B ARG* 3.4 28.3 + - - +
126B SER 4.8 2.0 - - - +
127B CYS* 3.5 26.2 - - + -
128B ASP* 3.2 20.7 + - - +
129B CYS 2.8 40.1 + - - +
130B LEU* 3.5 7.0 - - - +
131B GLN* 2.9 28.8 + - - +
132B GLY 3.9 0.3 + - - -
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Residues in contact with ILE 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ARG 3.5 0.2 + - - -
3B GLU* 1.3 73.0 - - - +
5B VAL* 1.3 76.3 + - - +
6B HIS 4.1 0.2 + - - -
49B VAL* 2.8 29.2 + - + +
50B TYR* 3.7 37.9 - - + +
62B ARG* 3.2 26.3 + - - +
131B GLN* 3.7 22.7 - - + +
132B GLY 3.5 8.3 - - - +
133B PHE 4.6 0.2 - - - -
134B GLN* 3.8 17.9 - - + +
240B LEU* 3.8 24.5 - - + -
250B LEU* 3.9 19.3 - - + -
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Residues in contact with VAL 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 1.3 73.4 - - - +
6B HIS* 1.3 63.4 + - - +
7B ILE* 4.4 5.1 - - + +
62B ARG* 3.8 25.8 - - + +
64B ILE* 4.1 25.8 - - + -
120B VAL* 4.8 3.6 - - + -
123B GLU* 4.4 11.7 - - + -
124B SER* 4.3 11.0 - - - +
127B CYS* 4.6 2.0 - - - -
130B LEU* 3.5 23.6 - - + -
132B GLY 3.1 6.4 + - - +
133B PHE* 3.3 28.9 - - + +
134B GLN 2.9 26.0 + - - +
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Residues in contact with HIS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE 4.1 0.2 - - - -
5B VAL* 1.3 72.0 - - - +
7B ILE* 1.3 69.3 + - - +
8B GLN* 2.8 32.6 + - + +
17B GLY* 4.4 2.9 - - - -
20B PHE* 4.4 8.7 - + - -
21B TRP* 3.2 34.3 + + + -
50B TYR* 5.1 2.9 - - + -
62B ARG 2.9 15.4 + - - +
63B ALA* 3.3 9.6 - - + -
64B ILE* 2.8 32.1 + - - +
134B GLN* 3.2 36.8 + - + +
136B THR* 3.7 30.5 - - + -
506B 8WR 4.8 0.2 - + - -
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Residues in contact with ILE 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.4 3.8 - - + +
6B HIS* 1.3 84.1 + - - +
8B GLN* 1.3 64.6 + - - +
9B ALA* 4.3 0.9 - - + +
64B ILE* 3.4 20.4 - - + +
66B VAL* 3.9 24.9 - - + -
116B VAL* 5.0 1.6 - - + -
120B VAL* 4.2 12.6 - - + -
133B PHE* 4.6 14.4 - - + -
134B GLN 3.0 9.5 + - - +
135B LEU* 3.2 26.3 - - + +
136B THR* 3.1 22.2 + - - -
151B LEU* 4.4 10.5 - - + -
155B ILE* 3.4 33.7 - - + -
164B MET* 5.7 0.9 - - + -
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B HIS* 2.8 26.6 + - + +
7B ILE* 1.3 71.9 - - - +
9B ALA* 1.3 55.1 + - - +
13B GLY 3.4 7.6 - - - +
14B ASN* 2.9 45.3 + - - +
17B GLY* 3.2 19.7 - - - +
18B ALA* 3.8 6.1 - - - +
21B TRP* 3.7 6.0 - - - -
64B ILE 2.9 16.7 + - - +
65B LEU* 3.5 22.9 - - + +
66B VAL* 2.8 34.8 + - - +
76B VAL* 4.7 2.2 - - - +
85B PHE* 5.1 2.1 - - - -
136B THR* 3.0 22.4 - - - +
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 5.2 0.2 - - + -
8B GLN* 1.3 73.8 - - - +
10B GLY* 1.3 66.0 + - - +
13B GLY* 3.4 15.0 + - - -
66B VAL* 3.3 19.3 - - + -
135B LEU* 4.9 6.5 - - + -
136B THR 3.0 13.1 + - - +
137B HIS* 3.8 2.8 - - + +
138B SER 4.8 0.2 + - - -
143B THR* 5.0 2.2 - - + +
144B GLY* 3.3 27.0 - - - +
147B MET* 6.0 0.4 - - + -
148B GLY* 4.4 17.0 - - - +
151B LEU* 4.9 4.9 - - + -
501B GDP 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