Contacts of the strand formed by residues 38 - 45 (chain A) in PDB entry 2YXS
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 THR 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASP* 6.5 0.4 - - + -
33A GLN 4.0 4.3 + - - +
34A LEU* 3.7 32.5 - - + -
35A ASP 2.7 30.1 + - - -
36A PRO 3.7 0.2 + - - -
37A GLY* 1.3 78.4 - - - +
39A LEU* 1.3 71.1 + - - +
40A ILE* 4.9 0.4 - - + -
114A ILE 3.6 0.7 - - - +
115A MSE 3.4 2.6 - - - -
116A VAL* 2.9 31.4 + - + +
158A PHE* 5.2 4.7 - - + -
159A SER 3.3 16.6 - - - +
160A GLY* 4.4 1.7 - - - -
161A PRO* 3.5 16.3 - - - +
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Residues in contact with LEU 39 (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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37A GLY 3.9 7.9 - - - +
38A THR* 1.3 78.6 - - - +
40A ILE* 1.3 63.2 + - - +
41A VAL* 4.0 13.0 - - + +
113A VAL* 4.1 17.3 - - + -
114A ILE 3.3 2.7 - - - +
115A MSE 3.5 43.7 - - + -
158A PHE* 3.4 5.9 - - - -
159A SER* 2.8 55.0 + - - +
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Residues in contact with ILE 40 (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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30A ILE* 5.1 0.7 - - + -
34A LEU* 4.0 29.4 - - + -
38A THR* 4.9 1.1 - - + -
39A LEU* 1.3 75.7 - - - +
41A VAL* 1.3 60.7 + - - +
42A ILE* 4.0 25.4 + - + +
57A LEU* 3.9 31.2 - - + -
112A ILE 3.4 3.8 - - - +
113A VAL* 3.5 0.3 - - - -
114A ILE* 2.9 50.7 + - + +
116A VAL* 4.6 7.0 - - + -
145A LEU* 5.0 7.0 - - + -
156A ILE* 5.2 0.9 - - + -
157A GLY 3.6 4.0 - - - +
158A PHE* 4.0 29.8 - - + -
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Residues in contact with VAL 41 (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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15A LEU* 3.8 39.2 - - + +
39A LEU* 4.6 11.7 - - + -
40A ILE* 1.3 74.6 - - - +
42A ILE* 1.3 66.0 + - - +
43A CYS* 4.3 11.9 - - - -
111A GLU* 4.3 21.5 - - + +
112A ILE 3.3 8.3 - - - +
113A VAL* 4.4 19.7 - - + -
155A SER* 3.8 1.9 + - - +
156A ILE* 3.5 3.8 - - - -
157A GLY 2.8 36.3 + - - +
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Residues in contact with ILE 42 (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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40A ILE* 4.1 22.4 - - + +
41A VAL* 1.3 78.4 - - - +
43A CYS* 1.3 62.2 + - - +
55A VAL* 3.8 36.6 - - + -
110A PHE* 3.9 8.6 - - + -
111A GLU* 3.6 0.7 - - - -
112A ILE* 2.8 52.0 + - + +
114A ILE* 4.9 5.6 - - + -
145A LEU* 4.5 6.3 - - + -
147A ILE* 4.2 12.1 - - + -
153A ILE* 3.8 31.6 - - + -
155A SER 3.5 7.9 - - - +
156A ILE* 4.5 10.1 - - + -
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Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 4.3 11.4 - - - -
42A ILE* 1.3 76.2 - - - +
44A GLY* 1.3 59.2 + - - +
110A PHE* 3.4 9.0 - - - +
111A GLU* 4.1 27.4 - - - -
153A ILE* 3.7 4.5 - - - +
154A HIS* 2.8 30.7 + - + +
155A SER* 3.0 32.2 + - - +
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Residues in contact with GLY 44 (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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43A CYS* 1.3 75.8 - - - +
45A HIS* 1.3 61.1 + - - +
109A SER* 3.3 7.1 - - - -
110A PHE* 2.8 45.9 + - - +
152A ASN 3.0 14.4 - - - -
153A ILE* 4.2 0.7 - - - -
154A HIS* 3.8 14.5 + - - -
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Residues in contact with HIS 45 (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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44A GLY* 1.3 73.9 - - - +
46A VAL* 1.3 83.8 + - - +
47A PRO* 3.4 5.1 - - + +
107A GLU* 3.2 31.1 + - - +
108A LYS* 3.5 13.9 - - - -
109A SER* 3.3 20.5 + - - -
110A PHE* 3.5 7.4 - - - -
151A VAL* 3.8 3.1 - - - +
152A ASN* 2.8 42.3 + - + +
154A HIS* 3.7 18.5 - + + +
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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