Contacts of the strand formed by residues 143 - 149 (chain H) in PDB entry 5T0G
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 ARG 143 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39H LYS* 6.1 0.7 - - - +
140H ASN 2.9 8.8 + - - +
141H GLU* 3.1 7.7 + - + +
142H GLY* 1.3 76.3 - - - +
144H PRO* 1.3 65.0 - - - +
145H TYR* 2.9 44.6 - - + +
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Residues in contact with PRO 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LYS* 3.1 34.1 - - - +
41H ALA 3.9 6.5 - - - +
42H ASN 3.1 23.8 - - - +
43H GLY* 3.6 17.3 - - - -
44H VAL* 4.1 5.4 - - + -
138H GLY 3.3 15.5 - - - +
139H TRP* 3.8 13.9 - - + -
142H GLY 3.3 10.5 - - - +
143H ARG* 1.3 89.0 - - - +
145H TYR* 1.3 69.2 + - - +
213H CYS 5.4 0.4 - - - +
215H GLU* 3.3 6.9 - - - +
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Residues in contact with TYR 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LYS* 4.4 3.4 - - - +
44H VAL* 3.2 16.7 - - - +
107H THR* 3.4 22.2 - - - +
108H ALA* 5.6 3.4 - - + -
137H CYS* 3.3 17.7 - - - -
138H GLY 2.9 9.4 + - - +
140H ASN* 3.5 26.7 + - + -
141H GLU* 5.1 4.5 - - - +
143H ARG* 2.9 36.7 + - + +
144H PRO* 1.3 80.8 - - + +
146H LEU* 1.3 60.1 + - - +
147H PHE* 3.5 29.2 - + + -
57I ASP* 5.5 0.9 - - - -
59I VAL* 4.2 32.3 - - + -
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Residues in contact with LEU 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H GLY* 4.2 19.7 - - - +
38H ILE 4.2 2.0 - - - +
39H LYS* 3.8 14.7 - - + +
44H VAL* 3.9 8.5 - - + -
46H LEU* 3.9 25.1 - - + -
135H LEU* 5.0 4.7 - - + -
136H ILE 3.3 17.9 - - - +
137H CYS* 4.2 0.7 - - + -
145H TYR* 1.3 75.4 - - - +
147H PHE* 1.3 77.2 + - - +
157H ALA* 3.4 18.2 - - - +
158H TRP* 3.2 29.2 + - + +
159H LYS 3.7 15.3 - - - +
161H THR* 4.4 14.8 - - + -
57I ASP* 3.9 6.6 + - - +
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Residues in contact with PHE 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H THR* 3.8 11.4 - - - -
108H ALA* 3.7 33.9 - - + -
111H VAL* 3.4 32.1 - - + -
135H LEU* 3.4 5.4 - - - +
136H ILE* 2.7 45.2 + - + +
145H TYR* 3.5 31.2 - + + -
146H LEU* 1.3 90.9 - - - +
148H GLN* 1.3 62.8 + - - +
155H TYR* 5.5 0.7 - - + -
156H PHE 3.1 15.7 - - - +
157H ALA* 4.1 7.2 - - + +
158H TRP* 5.7 0.9 - - - -
161H THR* 5.8 0.4 - - - +
57I ASP* 5.8 0.2 - - - -
59I VAL* 4.5 6.1 - - + -
60I PHE* 3.6 32.3 - + + -
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Residues in contact with GLN 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H VAL* 6.5 0.2 - - - -
133H SER* 5.2 5.2 - - - -
134H LEU 3.3 4.3 - - - -
135H LEU* 3.6 22.7 - - + +
136H ILE* 6.2 0.2 - - - -
147H PHE* 1.3 77.4 - - - +
149H SER* 1.3 72.7 + - - +
154H ALA 3.8 0.5 - - - +
155H TYR* 3.4 5.4 - - - -
156H PHE* 3.0 35.9 + - + +
158H TRP* 3.5 26.8 + - + +
161H THR* 2.7 29.7 + - + -
162H ALA 4.5 9.5 + - - -
163H MET* 5.0 7.1 - - - +
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Residues in contact with SER 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H VAL* 5.8 3.6 - - - -
115H ALA* 6.0 4.9 - - - -
118H MET* 5.1 6.3 - - - +
132H VAL 4.6 1.6 + - - -
133H SER* 3.3 19.8 - - - -
134H LEU* 2.7 52.7 + - - +
136H ILE* 5.1 9.3 - - - +
148H GLN* 1.3 84.8 + - - +
150H ASP* 1.3 67.7 + - - +
153H GLY* 5.6 2.0 - - - -
154H ALA 3.4 9.9 - - - -
155H TYR* 4.7 3.1 - - - +
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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