Contacts of the strand formed by residues 131 - 136 (chain T) in PDB entry 5A0Q
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 GLY 131 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T VAL* 3.8 18.4 - - - +
75T ALA 3.0 33.1 + - - +
129T GLY 3.6 2.6 + - - -
130T VAL* 1.4 77.0 - - - +
132T LEU* 1.3 58.8 + - - -
147T THR 3.4 10.1 - - - -
148T CYS* 4.9 0.2 - - - -
149T PRO* 4.4 5.4 - - - -
161T ILE* 3.2 12.7 - - - +
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Residues in contact with LEU 132 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72T ILE* 3.7 46.2 - - + -
73T SER 3.5 2.5 - - - +
74T ILE* 3.9 14.8 - - + -
81T ALA* 4.5 3.8 - - + -
84T LEU* 4.5 18.4 - - + -
88T MET* 5.4 2.5 - - + -
112T ILE* 4.5 8.5 - - + -
130T VAL* 3.5 35.4 - - + +
131T GLY* 1.3 72.7 - - - +
133T LEU* 1.3 59.2 + - - +
134T ILE* 3.9 13.2 - - + -
146T GLN* 3.3 6.9 - - - +
147T THR* 2.9 45.3 + - - +
161T ILE* 3.7 6.0 - - - +
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Residues in contact with LEU 133 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T THR 3.7 24.9 - - - +
36T VAL 4.2 0.2 - - - -
37T GLY* 3.9 18.4 - - - +
46T LEU* 3.8 9.4 - - + +
71T GLY 3.7 0.5 - - - +
72T ILE* 3.4 1.8 - - - -
73T SER* 3.0 44.7 + - - +
132T LEU* 1.3 72.8 - - - +
134T ILE* 1.3 61.1 + - - +
135T ALA 3.3 6.0 + - - +
144T ILE* 4.6 14.6 - - + -
145T PHE 3.8 2.5 - - - -
146T GLN* 3.9 25.8 - - + +
159T MET* 3.9 22.4 - - + -
160T SER* 4.3 1.6 - - - -
161T ILE* 3.9 24.0 - - + +
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Residues in contact with ILE 134 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70T ILE* 3.5 30.3 - - + -
71T GLY 3.9 2.9 - - - -
72T ILE* 3.7 20.0 - - + -
105T VAL* 4.1 6.7 - - + +
108T LEU* 4.9 6.3 - - + -
109T VAL* 4.0 21.1 - - + -
112T ILE* 3.4 22.9 - - + -
132T LEU* 4.0 7.4 - - + -
133T LEU* 1.3 66.9 - - - +
135T ALA* 1.4 58.8 + - - +
136T GLY 3.9 0.5 + - - -
143T HIS 4.1 0.5 - - - +
144T ILE* 3.5 1.9 - - - -
145T PHE* 2.9 41.9 + - - +
147T THR* 3.3 41.3 - - + +
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Residues in contact with ALA 135 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T ALA* 4.2 12.3 - - + -
45T VAL 5.1 0.4 - - - -
46T LEU* 3.7 33.2 - - + +
70T ILE* 3.5 4.5 - - - +
71T GLY 2.9 31.6 + - - +
133T LEU 3.3 3.6 + - - -
134T ILE* 1.4 75.7 - - - +
136T GLY* 1.3 59.7 + - - +
143T HIS 3.7 4.5 - - - -
144T ILE* 3.7 22.6 - - + +
221T PHE* 4.5 6.3 - - + -
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Residues in contact with GLY 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T ALA* 4.1 2.9 - - - +
69T HIS 3.5 11.4 - - - -
70T ILE* 4.0 10.5 - - - -
105T VAL* 4.0 8.3 - - - +
134T ILE 3.9 0.6 + - - -
135T ALA* 1.3 76.9 - - - +
137T TYR* 1.3 62.3 + - - -
142T PRO* 3.5 5.2 - - - +
143T HIS 2.8 33.4 + - - +
215T VAL* 4.2 7.6 - - - -
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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