Contacts of the strand formed by residues 142 - 147 (chain k) in PDB entry 5GJQ
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 PRO 142 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36k ARG* 3.2 21.5 + - + -
37k GLY 3.5 22.9 - - - +
38k ARG* 3.5 14.1 - - - +
41k VAL* 3.9 18.2 - - + -
135k GLY 3.5 6.7 - - - +
136k PHE* 3.5 24.7 - - + -
140k GLY 3.3 8.2 - - - +
141k THR* 1.3 86.7 - - - +
143k ARG* 1.3 67.3 + - - +
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Residues in contact with ARG 143 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36k ARG* 4.5 10.8 - - - +
41k VAL* 5.0 1.7 - - - +
103k THR* 5.7 2.4 + - - -
104k VAL* 4.2 14.0 - - + +
105k GLU* 5.6 8.0 + - - +
133k ILE 4.1 0.3 - - - +
134k VAL* 3.6 3.6 - - - +
135k GLY* 2.9 35.9 + - - +
137k ASP* 3.4 28.7 - - - +
139k ASP* 4.0 9.7 + - - -
141k THR* 3.7 26.6 + - - -
142k PRO* 1.3 81.3 - - - +
144k LEU* 1.3 60.9 + - - +
145k TYR* 4.0 34.1 - - + -
155k ALA* 5.9 4.3 - - + -
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Residues in contact with LEU 144 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34k GLY* 3.5 32.1 - - - +
35k VAL* 4.4 3.6 - - - +
36k ARG* 4.7 10.4 - - + +
41k VAL* 5.7 1.6 - - + -
132k LEU* 3.7 20.2 - - + -
133k ILE 3.4 15.5 - - - +
134k VAL* 3.5 21.1 - - + -
143k ARG* 1.3 76.5 - - - +
145k TYR* 1.3 65.7 + - - +
155k ALA* 3.3 5.8 - - - +
156k TRP* 2.8 53.8 + - + +
157k LYS 4.1 4.7 - - - +
158k ALA* 4.0 15.9 - - - +
159k ASN* 4.4 2.9 - - + +
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Residues in contact with TYR 145 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104k VAL* 4.3 8.7 - - + -
105k GLU* 3.0 47.0 + - + +
108k THR* 3.6 29.6 - - + +
132k LEU* 3.8 0.2 - - - -
133k ILE* 2.9 33.5 + - + +
143k ARG* 4.0 30.5 - - + -
144k LEU* 1.3 90.2 - - - +
146k GLN* 1.3 62.5 + - - +
153k TYR* 3.9 28.5 - + - -
154k HIS 3.2 21.1 - - - -
155k ALA* 3.6 19.9 - - + +
156k TRP* 4.7 0.7 - - - +
63l SER* 4.6 7.9 - - - -
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Residues in contact with GLN 146 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130k SER* 4.6 3.2 + - - -
131k ALA 3.3 11.9 - - - +
132k LEU* 3.7 15.0 - - + +
133k ILE* 5.8 0.2 - - - -
144k LEU* 5.5 0.2 - - + -
145k TYR* 1.3 76.8 - - - +
147k THR* 1.3 83.7 + - - +
148k ASP* 4.8 7.3 + - - +
152k THR 4.1 0.2 - - - +
153k TYR* 3.1 5.1 - - - +
154k HIS 2.9 31.4 + - - +
156k TRP* 4.0 14.1 - - + +
159k ASN* 2.9 30.0 + - - +
160k ALA 4.2 0.2 - - - +
161k ILE* 3.2 31.6 - - - +
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Residues in contact with THR 147 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108k THR* 3.8 33.4 - - + +
111k ILE* 4.5 3.7 - - + +
112k ALA* 4.5 10.5 - - + +
115k LYS* 2.5 35.1 + - - -
130k SER* 3.6 12.1 - - - -
131k ALA* 3.2 16.4 + - - +
133k ILE* 4.5 10.1 - - + -
146k GLN* 1.3 97.5 + - - +
148k ASP* 1.3 61.9 - - - +
152k THR 3.5 7.4 - - - -
153k TYR* 3.9 8.7 - - + -
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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