Contacts of the strand formed by residues 7 - 14 (chain A) in PDB entry 1YK1
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 LYS 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PRO 5.3 2.7 - - - +
6A GLN* 1.3 79.5 + - - +
8A ILE* 1.3 58.3 + - - +
9A GLU* 3.7 5.1 + - + +
53A ARG* 3.6 16.4 - - + +
55A GLN* 3.0 34.3 - - + +
84A ASP* 3.7 1.4 - - - +
337A LYS* 2.5 31.5 + - - +
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Residues in contact with ILE 8 (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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6A GLN* 3.8 23.1 - - + +
7A LYS* 1.3 73.0 - - - +
9A GLU* 1.3 62.9 + - - +
10A VAL* 4.0 8.8 + - + +
52A THR* 4.3 6.5 - - + -
53A ARG 2.9 12.0 + - - +
54A PHE* 3.5 35.5 - - + -
55A GLN* 2.9 26.9 + - - +
84A ASP* 3.5 11.2 - - + +
323A TYR* 3.5 32.8 - - + +
327A LEU* 3.8 22.4 - - + -
337A LYS* 4.0 16.2 - - + -
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Residues in contact with GLU 9 (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 LYS* 4.5 5.7 - - + +
8A ILE* 1.3 75.2 - - - +
10A VAL* 1.3 61.2 + - - +
55A GLN* 3.7 32.7 + - + +
74A ARG* 5.6 4.0 + - - -
82A LYS 5.6 3.0 - - - +
83A PRO* 3.7 11.2 - - + +
84A ASP* 2.6 49.2 + - - +
85A LEU 3.1 4.3 + - - -
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Residues in contact with VAL 10 (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 ILE* 4.2 13.0 - - + +
9A GLU* 1.3 75.7 - - - +
11A LEU* 1.3 60.5 + - - +
12A VAL* 4.7 5.6 - - + -
31A ILE* 6.1 0.4 - - + -
54A PHE* 4.7 10.8 - - + -
55A GLN 3.3 5.2 + - - +
56A VAL* 3.6 40.6 - - + -
57A ALA* 3.1 23.4 + - - +
83A PRO* 4.6 2.0 - - - -
85A LEU* 2.9 43.7 - - + +
87A LEU* 5.0 7.0 - - + -
320A ILE* 5.8 5.4 - - + -
323A TYR* 4.8 0.7 - - + -
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Residues in contact with LEU 11 (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* 1.3 72.7 - - - +
12A VAL* 1.3 77.4 + - - +
13A LEU* 3.6 30.7 + - + -
57A ALA* 3.8 8.5 - - + +
59A GLU* 4.1 8.3 - - + -
71A LEU* 3.6 40.2 - - + -
74A ARG* 4.4 25.8 - - - +
83A PRO* 4.1 17.0 - - + +
85A LEU 2.6 12.1 + - - +
86A ILE* 3.3 10.8 - - + +
87A LEU 2.9 24.4 + - - +
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Residues in contact with VAL 12 (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 1.7 + - + -
11A LEU* 1.3 78.5 - - - +
13A LEU* 1.3 61.1 - - - +
14A LEU* 4.0 14.8 - - + -
24A LEU* 3.4 28.3 - - + -
27A VAL* 5.7 2.7 - - + -
31A ILE* 5.1 4.9 - - + -
56A VAL* 3.9 13.0 - - + -
57A ALA 3.0 7.9 + - - +
58A TYR* 3.6 29.2 - - + -
59A GLU 3.0 27.4 + - - +
87A LEU* 3.6 34.3 - - + +
316A PHE* 6.4 0.2 - - + -
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Residues in contact with LEU 13 (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 LEU* 3.6 27.1 - - + +
12A VAL* 1.3 75.1 - - - +
14A LEU* 1.3 67.4 + - - +
59A GLU* 3.5 25.6 - - + +
60A ASP 4.8 2.2 - - - +
61A SER* 3.9 3.8 - - - -
67A ALA* 3.9 32.3 - - + +
70A SER* 3.5 22.4 - - - +
71A LEU* 4.5 1.3 - - + -
86A ILE* 4.5 4.3 - - + -
87A LEU 2.8 13.4 + - - +
88A GLY* 3.6 0.7 - - - -
89A PRO* 3.1 36.0 - - + +
98A VAL* 4.2 23.6 - - + -
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Residues in contact with LEU 14 (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* 4.0 9.1 - - + -
13A LEU* 1.3 84.1 - - - +
15A PRO* 1.3 69.5 - - + +
22A PHE 3.3 17.7 - - - +
23A SER 4.0 1.1 - - - +
24A LEU* 3.7 25.9 - - + +
27A VAL* 3.4 36.6 - - + -
59A GLU 3.4 5.5 + - - +
60A ASP* 3.3 7.1 - - - -
61A SER* 2.6 29.8 + - - -
87A LEU 5.0 0.2 - - - +
88A GLY* 4.4 2.0 - - - -
90A VAL* 3.7 31.6 - - + +
316A PHE* 3.9 15.0 - - + -
513A CL 4.0 0.4 - - - -
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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