Contacts of the strand formed by residues 134 - 138 (chain J) in PDB entry 2YGD
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 134 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I LEU 4.1 7.9 - - - -
132I THR* 3.8 20.4 - - - +
134I THR* 3.6 26.9 - - + +
148I PRO* 5.6 3.1 - - + -
131J LEU 4.7 0.9 - - - +
132J THR 3.8 4.2 + - - +
133J ILE* 1.3 74.1 - - - +
135J SER* 1.3 69.7 + - - +
146J ASN* 2.8 42.0 + - - -
147J GLY* 4.9 2.8 - - - -
148J PRO* 5.8 0.7 - - - +
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Residues in contact with SER 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I PRO 4.3 5.4 + - - -
131I LEU* 2.8 43.9 + - - +
151I GLN* 2.9 20.6 + - - -
91J VAL* 5.5 2.5 - - - +
98J ILE* 5.7 0.2 - - - +
133J ILE* 4.9 1.4 + - - +
134J THR* 1.3 80.9 + - - +
136J SER* 1.3 63.6 + - - +
143J LEU* 4.5 1.1 - - - +
144J THR 3.2 13.7 - - - -
145J VAL* 3.4 18.1 - - - +
146J ASN* 3.3 9.5 + - - +
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Residues in contact with SER 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I LEU* 3.9 3.1 - - - +
151I GLN* 4.1 16.6 - - - +
135J SER* 1.3 77.0 - - - +
137J LEU* 1.3 68.1 + - - +
143J LEU* 3.7 8.3 - - - +
144J THR* 2.8 36.8 + - - +
146J ASN* 2.5 21.6 + - - -
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I LEU* 4.0 10.8 - - + -
151I GLN* 3.6 9.4 - - - +
160I PRO* 3.1 29.2 - - + +
161I ILE 4.3 1.8 - - - -
162I THR* 3.1 27.6 - - + +
163I ARG* 3.6 32.6 - - + +
86J PRO* 4.0 12.6 - - + -
136J SER* 1.3 81.4 + - - +
138J SER* 1.3 77.5 + - - +
139J SER* 4.2 0.9 - - - +
141J GLY 6.0 0.2 - - - -
142J VAL* 3.1 16.8 - - - +
143J LEU* 4.2 10.1 - - + -
144J THR* 4.3 7.6 - - - +
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Residues in contact with SER 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163I ARG* 4.3 17.8 + - - -
86J PRO* 4.0 1.4 - - - +
137J LEU* 1.3 83.8 - - - +
139J SER* 1.3 59.3 + - - +
140J ASP* 3.0 14.7 + - - +
141J GLY* 3.2 2.6 + - - -
142J VAL* 2.8 41.9 + - - +
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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