Contacts of the strand formed by residues 15 - 24 (chain B) in PDB entry 3T5G
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 PHE 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.0 21.6 + - + +
12B LEU* 3.2 22.1 + - + +
13B ARG 3.4 2.3 - - - +
14B GLY* 1.3 78.5 - - - +
16B LYS* 1.3 63.2 + - - +
17B LEU* 3.8 23.6 - - + -
37B ASP* 4.6 2.3 - - - +
39B SER* 3.7 32.1 + - - -
65B PHE* 3.6 25.4 - + + -
66B SER 3.4 9.6 - - - -
67B SER* 4.4 3.8 - - - +
71B MET* 4.3 16.2 - - + -
74B PHE* 3.6 33.7 - + - -
133B PHE* 3.9 15.5 - + + -
140B VAL* 5.8 2.2 - - + -
141B SER* 5.6 3.8 - - - -
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Residues in contact with LYS 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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14B GLY 5.2 2.2 - - - +
15B PHE* 1.3 83.5 - - - +
17B LEU* 1.3 62.6 + - - +
18B ASN* 2.8 31.2 + - - +
37B ASP* 3.5 14.8 - - - +
65B PHE* 3.2 5.7 - - - +
66B SER* 2.9 58.2 + - - -
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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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2010A FAR 4.0 26.0 - - + -
15B PHE* 3.8 13.9 - - + -
16B LYS* 1.3 71.8 - - - +
18B ASN* 1.3 65.4 + - - +
19B TRP* 5.1 4.7 - - - +
20B MET* 5.7 4.3 - - + -
35B THR 4.4 2.3 - - - +
36B GLU 4.7 2.6 - - - +
37B ASP* 3.3 38.6 + - - +
38B LEU* 4.2 7.2 - - + +
39B SER* 3.7 29.3 + - - +
63B LEU* 4.7 24.5 - - + -
64B ASN 3.6 5.4 - - - +
65B PHE* 3.8 22.2 - - + -
133B PHE* 4.9 3.8 - - + -
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Residues in contact with ASN 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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16B LYS* 2.8 42.5 - - - +
17B LEU* 1.3 73.2 - - - +
19B TRP* 1.3 68.9 + - + +
35B THR* 3.5 25.1 - - - +
36B GLU 5.9 0.2 - - - -
64B ASN* 2.8 35.3 + - - +
65B PHE 3.7 0.2 - - - -
66B SER* 2.9 27.5 + - - -
102B THR* 3.7 2.4 - - - +
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Residues in contact with TRP 19 (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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17B LEU* 3.7 3.9 - - - +
18B ASN* 1.3 84.8 + - + +
20B MET* 1.3 68.8 + - - +
21B ASN* 3.4 31.4 - - - +
34B GLY 3.4 14.6 - - - +
35B THR* 4.1 11.7 - - + +
36B GLU 6.0 0.7 - - - -
62B GLU* 3.8 20.6 - - + -
63B LEU* 3.9 0.9 - - - +
64B ASN* 2.9 65.8 + - + +
104B THR* 3.9 22.7 - - + -
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Residues in contact with MET 20 (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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2010A FAR 3.6 42.4 - - + -
17B LEU* 5.7 4.9 - - + -
19B TRP* 1.3 78.3 - - - +
21B ASN* 1.3 71.3 + - - +
22B LEU* 4.1 7.2 - - + -
32B TRP* 3.5 29.2 - - + -
33B GLN* 3.2 4.7 - - - +
34B GLY 3.0 32.6 + - - +
38B LEU* 4.9 5.4 - - + -
61B ARG* 3.5 24.2 - - + -
62B GLU 3.0 13.7 - - - +
63B LEU* 3.1 28.5 - - + -
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Residues in contact with ASN 21 (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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19B TRP* 3.4 19.1 - - - -
20B MET* 1.3 80.4 - - - +
22B LEU* 1.3 63.1 + - - +
23B ARG* 3.4 26.7 - - + +
30B ILE* 4.3 10.9 - - + +
32B TRP* 3.5 6.1 - - - +
33B GLN* 3.5 20.4 - - - +
61B ARG* 3.4 11.6 - - - +
62B GLU* 2.7 60.9 + - + +
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Residues in contact with LEU 22 (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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2010A FAR 3.7 36.6 - - + -
20B MET* 4.1 3.4 - - + -
21B ASN* 1.3 73.6 - - - +
23B ARG* 1.3 55.9 + - - +
30B ILE* 3.7 2.1 - - - -
31B LEU* 2.8 32.8 + - - -
32B TRP* 2.8 44.7 + - + +
49B VAL* 4.3 8.5 - - + -
53B ILE* 3.9 22.4 - - + -
59B VAL* 3.9 13.9 - - + -
60B SER 3.6 1.6 - - - -
61B ARG* 3.6 38.8 - - + -
109B ILE* 5.0 0.9 - - + -
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Residues in contact with ARG 23 (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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21B ASN* 3.4 15.4 - - + +
22B LEU* 1.3 77.7 - - - +
24B ASP* 1.3 61.4 + - - +
25B ALA 3.2 0.2 + - - -
28B GLY* 2.8 38.6 + - - +
29B LYS 3.2 7.0 - - - +
30B ILE* 3.7 29.5 - - + +
31B LEU* 4.3 4.9 - - - +
59B VAL* 3.3 7.7 - - - +
60B SER* 2.8 49.9 + - - +
62B GLU* 3.1 36.4 + - - -
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Residues in contact with ASP 24 (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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23B ARG* 1.3 69.2 - - - +
25B ALA* 1.3 56.8 + - - +
26B GLU* 3.0 25.8 + - - +
27B THR* 3.3 22.1 + - - +
28B GLY* 2.7 35.2 + - - -
29B LYS* 3.0 11.4 + - + +
31B LEU* 3.9 20.6 - - + +
56B CYS* 3.7 22.2 - - - +
57B LYS 6.0 0.4 - - - -
58B ALA 4.1 5.9 - - - +
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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