Contacts of the helix formed by residues 2 - 18 (chain B) in PDB entry 1YLA
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 ALA 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 75.9 - - - +
3B ASN* 1.3 64.5 + - - +
4B ILE* 3.4 15.5 - - + +
5B ALA* 3.2 7.1 + - + +
6B VAL* 2.9 25.1 + - - +
64B GLU* 4.6 10.9 + - - +
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Residues in contact with ASN 3 (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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1B MET 3.9 0.4 + - - -
2B ALA* 1.3 73.0 - - - +
4B ILE* 1.3 61.9 + - - +
6B VAL* 3.4 5.3 + - - +
7B GLN* 2.8 61.9 + - - +
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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 ALA* 4.6 11.0 - - + -
3B ASN* 1.3 83.1 - - - +
5B ALA* 1.3 67.3 + - + +
7B GLN* 4.0 4.3 - - - +
8B ARG* 3.2 28.2 + - + +
64B GLU 5.8 1.1 - - - +
66B TYR 4.0 12.1 - - - +
67B PRO* 4.1 12.6 - - + -
68B PHE* 3.8 33.4 - - + -
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Residues in contact with ALA 5 (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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1B MET* 4.0 25.6 - - + -
2B ALA* 3.2 10.4 + - + +
4B ILE* 1.3 81.3 - - + +
6B VAL* 1.3 65.4 + - - +
8B ARG* 3.4 3.0 + - - +
9B ILE* 3.0 29.1 + - - +
64B GLU 4.3 11.0 - - - +
66B TYR* 3.6 30.6 - - + +
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Residues in contact with VAL 6 (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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0B SER* 4.9 5.8 - - - +
1B MET* 3.4 31.4 - - + +
2B ALA 2.9 20.6 + - - +
3B ASN* 4.0 4.7 - - - +
5B ALA* 1.3 74.6 - - - +
7B GLN* 1.3 57.6 + - - +
9B ILE* 3.3 5.0 + - - +
10B LYS* 2.8 57.0 + - + +
35B ASN 5.0 2.9 - - - +
36B PHE* 4.0 24.2 - - + -
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Residues in contact with GLN 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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3B ASN* 2.8 47.5 + - - +
4B ILE* 4.0 4.9 - - - +
6B VAL* 1.3 76.3 - - - +
8B ARG* 1.3 65.8 + - + +
10B LYS* 3.8 19.9 - - - +
11B ARG* 3.0 34.3 + - - +
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Residues in contact with ARG 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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4B ILE* 3.2 23.3 + - + +
5B ALA 3.7 3.6 - - - +
7B GLN* 1.3 79.8 - - + +
9B ILE* 1.3 52.9 + - - +
11B ARG* 3.0 22.9 + - - +
12B GLU* 2.6 71.4 + - - +
66B TYR* 4.0 14.5 + - + -
67B PRO* 3.5 34.5 - - + +
102B ALA* 2.8 25.8 + - - +
103B ALA* 4.2 5.4 + - - +
104B MET 2.9 23.2 + - - -
105B THR* 4.4 2.8 - - - +
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Residues in contact with ILE 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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1B MET* 4.6 6.5 - - + -
5B ALA 3.0 19.3 + - - +
6B VAL* 3.8 4.0 - - - +
8B ARG* 1.3 75.9 - - - +
10B LYS* 1.3 52.8 + - - +
12B GLU* 3.9 3.0 - - - +
13B PHE* 2.7 36.5 + - + +
36B PHE* 3.4 39.5 - - + +
39B LEU* 4.6 9.4 - - + -
62B ILE* 3.5 46.9 - - + -
66B TYR* 3.6 20.4 - - + -
106B LEU* 4.4 11.6 - - + +
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Residues in contact with LYS 10 (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 VAL* 2.8 37.9 + - - +
7B GLN* 3.8 20.4 - - - +
9B ILE* 1.3 73.3 - - - +
11B ARG* 1.3 59.0 + - - +
13B PHE* 3.7 6.5 - - - +
14B LYS* 3.1 29.1 + - - +
36B PHE* 3.4 38.9 - - + -
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Residues in contact with ARG 11 (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 GLN* 3.0 26.0 + - - +
8B ARG* 3.4 24.1 - - - +
10B LYS* 1.3 74.4 - - - +
12B GLU* 1.3 67.5 + - - +
14B LYS* 3.4 31.8 + - - +
15B GLU* 3.0 29.6 + - + +
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Residues in contact with GLU 12 (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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8B ARG* 2.6 66.3 + - - +
9B ILE* 3.9 1.7 - - - +
11B ARG* 1.3 78.5 - - + +
13B PHE* 1.3 65.4 + - - +
15B GLU* 3.4 9.1 + - - +
16B VAL* 3.1 29.3 + - - +
66B TYR* 2.5 33.7 + - - -
104B MET 3.8 0.2 - - - +
105B THR* 3.8 21.5 - - + +
106B LEU* 3.2 29.8 + - + +
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Residues in contact with PHE 13 (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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176A ARG* 5.0 14.6 - - + -
9B ILE* 2.7 24.0 + - + +
10B LYS* 3.7 7.4 - - - +
12B GLU* 1.3 74.0 - - - +
14B LYS* 1.3 60.1 + - - +
16B VAL* 3.7 2.1 + - - +
17B LEU* 2.9 57.5 + - + +
29B VAL* 3.7 31.6 - - + -
30B ASP* 3.6 30.5 - - - -
31B LEU* 3.7 22.4 - - + -
36B PHE* 4.8 9.9 - + + -
39B LEU* 3.8 15.9 - - + -
106B LEU* 4.0 8.2 - - + +
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Residues in contact with LYS 14 (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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10B LYS 3.1 11.8 + - - +
11B ARG* 3.4 39.5 - - - +
13B PHE* 1.3 77.0 - - - +
15B GLU* 1.3 69.2 + - + +
17B LEU* 3.1 12.4 + - - +
18B LYS* 3.1 50.7 + - + +
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Residues in contact with GLU 15 (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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11B ARG* 3.0 19.3 + - + +
12B GLU* 3.4 10.3 + - - +
14B LYS* 1.3 79.1 - - + +
16B VAL* 1.3 63.5 + - - +
18B LYS* 3.2 7.8 + - - +
19B SER* 3.0 24.9 + - - -
105B THR* 3.6 30.0 + - - +
107B ARG* 3.7 39.4 + - - +
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Residues in contact with VAL 16 (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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12B GLU 3.1 16.9 + - - +
13B PHE 3.8 1.1 - - - +
15B GLU* 1.3 76.1 - - - +
17B LEU* 1.3 62.1 + - + +
19B SER* 2.7 15.1 + - - -
22B THR* 2.5 34.6 + - - +
27B ILE* 4.7 6.5 - - + -
28B LYS* 4.0 7.6 - - - +
29B VAL* 3.5 44.6 - - + +
106B LEU* 4.1 6.7 - - + -
107B ARG* 3.9 33.2 - - + +
110B LEU* 5.2 4.0 - - + -
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Residues in contact with LEU 17 (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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167A GLU* 4.9 3.5 - - + +
170A CYS* 6.0 1.1 - - - -
176A ARG* 3.5 43.3 - - - +
13B PHE* 2.9 50.5 - - + +
14B LYS* 3.1 9.8 + - - +
16B VAL* 1.3 82.2 - - + +
18B LYS* 1.3 64.0 + - + +
19B SER 3.6 2.1 + - - +
22B THR* 4.2 18.1 - - + +
23B SER 5.5 0.5 + - - -
28B LYS* 6.0 0.7 - - + -
29B VAL* 3.8 23.3 - - + +
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Residues in contact with LYS 18 (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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167A GLU* 3.6 43.1 - - + +
14B LYS* 3.1 43.4 + - + +
15B GLU* 3.2 6.5 + - - +
17B LEU* 1.3 79.0 - - + +
19B SER* 1.3 62.1 + - - +
20B GLU 4.1 0.7 + - - -
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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