Contacts of the strand formed by residues 117 - 128 (chain B) 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 GLY 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 3.6 6.6 - - - -
60B ARG* 3.8 4.5 - - - -
62B LYS* 3.8 16.8 - - - -
116B SER* 1.3 80.5 + - - +
118B ASP* 1.3 61.1 + - - -
119B TYR* 4.2 1.3 + - - -
143B HIS* 2.9 27.8 - - - -
144B ILE* 3.1 19.3 + - - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR 4.2 0.3 - - - +
59B PHE* 3.2 4.9 - - - -
60B ARG* 2.1 84.9 + - + +
67B PHE* 4.3 8.8 - - + -
117B GLY* 1.3 74.6 - - - -
119B TYR* 1.3 62.8 + - - +
120B GLU* 5.3 1.8 - - + +
141B LYS* 6.6 0.4 - - - -
142B ILE 3.9 1.7 - - - -
143B HIS* 3.4 27.0 - - - +
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Residues in contact with TYR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.9 22.0 - - + -
57B TRP* 4.1 22.9 - + + -
58B THR 3.7 3.6 - - - -
59B PHE* 3.1 44.8 - + + -
70B ILE* 4.1 8.3 - - + -
86B PHE* 2.6 36.2 - + - -
106B ILE* 5.4 2.5 - - + -
108B ILE* 4.1 5.1 - - + +
115B HIS* 4.0 11.2 + - - +
117B GLY 4.4 2.2 - - - -
118B ASP* 1.3 74.0 - - - +
120B GLU* 1.3 59.8 + - - +
141B LYS* 3.0 5.0 - - - +
142B ILE* 2.4 61.8 + - + +
144B ILE* 3.8 28.7 - - + +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU 4.0 0.7 - - - +
57B TRP* 3.5 2.3 - - - -
58B THR* 2.8 42.6 + - - +
67B PHE* 2.8 45.6 - - + -
118B ASP* 5.3 2.3 - - + +
119B TYR* 1.3 78.5 - - - +
121B CYS* 1.3 61.5 + - - +
122B HIS* 3.9 18.9 - - + -
139B VAL* 4.4 3.6 - - + +
140B LYS 3.8 3.4 - - - +
141B LYS* 2.8 38.5 + - + +
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Residues in contact with CYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B CYS* 2.0 47.8 - - - -
55B THR* 4.7 5.4 - - - -
56B GLU 3.4 5.8 - - - +
57B TRP* 3.6 32.8 - - + +
119B TYR 4.2 0.2 - - - -
120B GLU* 1.3 70.4 - - - +
122B HIS* 1.3 59.7 + - - +
123B VAL* 4.5 10.0 - - - +
138B VAL 4.0 0.5 - - - +
139B VAL* 3.6 0.2 - - - -
140B LYS* 2.4 57.0 + - - +
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Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 3.2 5.5 - - - +
56B GLU* 2.9 48.3 + - + +
58B THR* 3.8 20.7 + - + +
120B GLU* 3.9 35.2 - - + -
121B CYS* 1.3 76.4 - - - +
123B VAL* 1.3 61.7 + - - +
124B TYR* 3.8 31.2 - - + +
137B SER* 5.3 0.9 - - - +
138B VAL 3.6 7.0 - - - +
139B VAL* 3.7 21.7 - - + +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B CYS* 5.0 1.3 - - - -
42B SER* 4.3 22.7 - - - +
53B THR* 3.3 31.9 - - + -
54B PHE 3.8 3.1 - - - +
55B THR* 4.1 6.7 - - - +
104B LEU* 4.5 12.1 - - + -
121B CYS* 4.5 15.0 - - - -
122B HIS* 1.3 77.6 - - - +
124B TYR* 1.3 71.9 + - - +
125B ARG* 4.7 6.9 - - + +
136B THR 3.4 1.4 - - - +
137B SER* 3.4 19.1 - - - -
138B VAL* 3.1 34.2 + - + +
140B LYS* 5.6 1.8 - - + -
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU 3.8 0.7 - - - +
53B THR* 3.2 5.0 - - - +
54B PHE* 2.5 100.0 + + + -
56B GLU* 4.3 20.2 + - + -
122B HIS* 3.8 32.1 - - + +
123B VAL* 1.3 85.3 - - - +
125B ARG* 1.3 58.6 + - - +
135B ASN* 4.7 2.7 - - - +
136B THR 3.6 3.4 - - - +
137B SER* 4.1 23.8 - - - -
304B NAG 3.5 26.0 - - + +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLU* 4.2 14.0 + - - -
42B SER* 2.7 42.4 + - - -
43B CYS 4.4 1.2 - - - -
44B LYS* 3.9 27.5 - - - +
51B ALA* 4.2 6.7 - - + -
52B GLU 3.3 2.2 - - - -
53B THR* 2.8 31.4 + - + +
100B ASP* 4.2 9.7 + - - -
102B GLN 4.3 7.5 - - - +
123B VAL* 4.9 6.6 - - + +
124B TYR* 1.3 72.6 - - - +
126B LEU* 1.3 60.2 + - - +
127B LEU* 3.6 30.1 + - + +
134B HIS 3.2 13.2 - - - +
135B ASN* 3.6 7.0 + - - +
136B THR* 3.4 29.9 + - - +
138B VAL* 5.1 8.3 - - + +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ALA* 2.5 11.6 - - - +
52B GLU* 2.5 55.4 + - + +
125B ARG* 1.3 71.5 - - - +
127B LEU* 1.3 55.8 + - - +
128B PHE* 3.0 35.5 - - + -
133B GLU* 3.6 23.1 - - + +
134B HIS 3.7 20.4 - - - +
135B ASN* 4.7 15.7 - - + +
304B NAG 5.4 2.0 - - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A PRO* 6.0 0.4 - - + -
326A GLU* 4.1 39.7 - - + +
44B LYS* 4.6 4.0 - - + -
49B THR* 4.5 14.8 - - - +
50B ASN 4.6 0.7 - - - +
51B ALA* 2.3 45.1 - - + +
125B ARG* 3.6 17.5 - - - +
126B LEU* 1.3 72.8 - - - +
128B PHE* 1.3 63.6 + - - +
129B PHE* 3.8 23.2 + - + -
132B TYR 3.9 0.2 - - - +
133B GLU* 3.5 7.4 - - - +
134B HIS* 3.0 34.7 + - + +
136B THR* 4.2 18.8 - - - +
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 5.5 1.2 - - - -
50B ASN* 3.3 38.4 + - - +
51B ALA* 4.4 0.7 - - - -
52B GLU* 3.9 25.8 - - + -
126B LEU* 3.0 50.3 - - + -
127B LEU* 1.3 77.0 - - - +
129B PHE* 1.3 70.0 + - - +
132B TYR 4.2 1.3 - - - -
133B GLU* 3.7 26.0 - - + +
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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