Contacts of the strand formed by residues 129 - 134 (chain B) in PDB entry 1SHY
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 GLN 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B VAL* 3.5 3.8 - - - +
123B ASP* 2.9 55.6 + - + +
126B TYR* 4.5 6.2 - - - +
127B ASP 3.2 15.5 + - - +
128B ASP* 1.3 75.1 - - - +
130B LEU* 1.3 62.1 + - - +
131B ILE* 3.6 17.9 + - + +
143B ARG* 2.9 45.8 + - + +
144B HIS 3.3 13.7 - - - +
145B VAL* 4.2 9.0 - - - +
146B PHE* 3.9 9.0 - - - -
219B LEU* 4.2 12.0 - - - +
223B LYS* 4.3 6.6 - - - +
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Residues in contact with LEU 130 (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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56B ILE* 4.9 5.6 - - + -
63B PHE* 3.8 32.1 - - + -
70B ILE* 4.5 10.3 - - + -
120B LEU* 3.8 30.5 - - + -
121B VAL 3.3 22.0 - - - +
122B VAL* 3.7 19.1 - - + +
129B GLN* 1.3 72.5 - - - +
131B ILE* 1.3 59.5 + - - +
143B ARG* 3.3 2.8 - - - -
144B HIS* 2.6 61.9 + - + +
146B PHE* 4.1 12.7 - - + -
154B ILE* 3.8 9.6 - - + -
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Residues in contact with ILE 131 (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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120B LEU* 3.6 2.4 - - - +
121B VAL* 2.7 45.5 + - + +
123B ASP* 4.1 17.7 - - + -
129B GLN* 3.6 26.7 - - + +
130B LEU* 1.3 77.6 - - - +
132B SER* 1.3 63.0 + - - +
133B CYS* 4.3 4.6 - - - -
141B CYS* 4.3 19.3 - - + -
142B GLN 3.4 4.3 - - - +
143B ARG* 4.2 13.0 - - + -
161B ILE* 5.2 4.7 - - + -
193B ILE* 5.6 0.9 - - + -
195B PHE* 4.0 37.0 - - + -
219B LEU* 4.8 12.3 - - + -
226B PHE* 5.0 3.8 - - + -
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Residues in contact with SER 132 (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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70B ILE* 3.6 15.5 - - - +
117B ASN* 4.2 4.9 - - - -
119B ALA 3.7 5.8 - - - -
120B LEU* 3.6 22.2 - - - -
130B LEU 4.0 0.4 + - - -
131B ILE* 1.3 75.3 - - - +
133B CYS* 1.3 65.3 + - - +
134B GLY 4.1 1.3 + - - -
141B CYS* 3.1 1.2 - - - -
142B GLN* 2.9 42.2 + - - +
144B HIS* 3.4 21.6 + - - -
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Residues in contact with CYS 133 (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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117B ASN* 4.4 2.2 - - - -
118B MET* 3.0 27.3 + - - +
119B ALA* 3.1 33.7 + - + -
121B VAL* 6.3 0.9 - - - -
131B ILE* 4.3 9.2 - - - -
132B SER* 1.3 76.7 - - - +
134B GLY* 1.3 60.5 + - - +
140B THR 5.1 0.4 - - - -
141B CYS* 2.0 51.6 - - - +
176B VAL* 4.9 3.6 - - - -
177B VAL* 4.0 15.5 - - + -
184B VAL* 5.5 0.9 - - - -
195B PHE* 5.2 5.4 - - - -
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Residues in contact with GLY 134 (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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115B ASN* 3.6 16.6 - - - -
116B ILE 3.6 6.7 - - - -
117B ASN* 4.6 3.1 - - - -
118B MET* 4.0 0.9 - - - -
132B SER 4.1 1.8 + - - -
133B CYS* 1.3 72.7 - - - +
135B SER* 1.3 61.6 + - - -
136B VAL* 3.2 7.1 + - - -
137B ASN 5.3 0.2 - - - -
139B GLY* 3.5 10.9 - - - -
140B THR 4.0 10.0 + - - -
177B VAL* 3.1 17.4 - - - +
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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