Contacts of the strand formed by residues 137 - 146 (chain C) in PDB entry 6J8G
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 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C MET* 2.4 10.7 - - - +
128C TYR* 2.1 66.4 - - - +
129C ILE 3.3 15.5 - - - +
130C MET* 4.2 16.4 - - + +
135C ARG 3.8 1.3 + - - +
136C HIS* 1.3 73.3 - - - +
138C GLY* 1.3 67.3 + - - +
139C HIS* 3.9 4.4 + - - +
301C NAG 3.6 33.7 + - - -
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Residues in contact with GLY 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C MET* 2.3 37.3 - - - -
32C VAL* 3.8 10.3 - - - -
127C CYS 4.2 0.4 - - - -
128C TYR* 3.3 5.5 - - - +
129C ILE* 2.7 34.7 + - - -
137C ARG* 1.3 75.1 - - - +
139C HIS* 1.3 60.7 + - - +
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Residues in contact with HIS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C VAL* 3.4 17.0 - - - +
126C ASN* 2.8 30.1 + - + -
127C CYS 3.2 8.7 - - - -
128C TYR* 3.7 31.5 + + + -
137C ARG* 3.9 5.3 + - - +
138C GLY* 1.3 75.5 - - - +
140C GLY* 1.3 73.1 + - - +
141C LYS* 4.1 19.4 + - + +
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Residues in contact with GLY 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C VAL* 3.5 21.9 - - - +
34C VAL* 3.5 13.5 - - - -
125C TYR 3.8 0.4 - - - +
126C ASN* 3.3 1.9 - - - -
127C CYS* 2.8 37.9 + - - -
139C HIS* 1.3 80.6 - - - +
141C LYS* 1.3 60.3 + - - -
142C ILE* 4.3 0.9 - - - -
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Residues in contact with LYS 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 3.4 14.1 - - - +
35C PRO 3.9 1.7 - - - +
36C ALA* 4.1 9.2 - - - +
70C GLN* 4.7 5.8 + - - -
73C ASN 5.7 2.8 + - - -
124C ILE* 3.3 32.1 - - + +
125C TYR 3.4 2.7 - - - -
126C ASN* 3.3 20.4 - - - +
139C HIS* 4.1 17.8 + - + +
140C GLY* 1.3 74.2 - - - +
142C ILE* 1.3 62.0 + - - +
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Residues in contact with ILE 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 2.9 35.9 - - + -
35C PRO* 3.4 21.5 - - + +
38C LEU* 3.8 29.8 - - + -
48C LEU* 3.9 37.2 - - + -
49C PRO 4.4 1.6 - - - +
67C TRP* 4.2 16.8 - - + -
124C ILE* 3.4 6.0 - - - +
125C TYR* 2.8 44.7 + - + +
127C CYS* 5.7 0.4 - - - -
140C GLY 5.4 0.9 - - - -
141C LYS* 1.3 73.6 - - - +
143C HIS* 1.3 66.9 + - - +
144C LEU* 3.7 3.9 + - + +
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Residues in contact with HIS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA 2.9 18.6 + - - +
37C THR* 3.4 12.5 + - - +
38C LEU 2.8 26.7 + - - +
122C GLU* 4.9 7.1 - - - +
123C GLY* 3.4 17.2 + - - -
124C ILE* 3.5 22.1 - - + +
141C LYS 4.3 0.2 - - - -
142C ILE* 1.3 71.0 - - - +
144C LEU* 1.3 65.9 + - - +
145C GLN* 3.2 35.5 + - + +
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C LEU* 3.3 40.8 - - + +
40C VAL* 3.8 25.6 - - + -
46C ALA* 4.4 3.8 - - + -
48C LEU* 4.1 9.2 - - + -
114C LEU* 4.2 14.8 - - + -
117C VAL* 5.1 0.9 - - + -
121C ASP* 3.7 17.3 - - + +
122C GLU* 3.3 8.3 - - - +
123C GLY 2.9 28.6 + - - +
125C TYR* 3.6 40.8 - - + +
142C ILE* 3.7 3.9 + - + -
143C HIS* 1.3 73.2 - - - +
145C GLN* 1.3 61.4 + - - +
146C VAL* 4.8 2.5 - - + -
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Residues in contact with GLN 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C THR* 3.6 11.3 - - - +
38C LEU 2.8 6.3 + - - +
39C ASN* 2.8 33.3 + - + +
40C VAL* 3.0 29.4 + - - +
122C GLU* 3.6 12.6 - - - +
143C HIS* 3.2 40.0 - - + +
144C LEU* 1.3 77.6 - - - +
146C VAL* 1.3 64.5 + - - +
147C LEU 4.0 0.2 - - - -
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Residues in contact with VAL 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.3 13.5 - - + +
41C LEU 4.6 0.4 - - - -
42C ASN* 3.8 27.4 - - + +
117C VAL* 4.9 4.3 - - + -
118C GLN 3.5 19.7 - - - +
119C PRO* 3.9 24.0 - - + +
121C ASP* 4.5 4.7 - - + -
122C GLU* 3.2 35.3 + - - +
144C LEU* 4.8 3.8 - - + -
145C GLN* 1.3 76.9 - - - +
147C LEU* 1.3 76.8 + - - +
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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