Contacts of the strand formed by residues 119 - 128 (chain B) in PDB entry 6D6Q
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 GLN 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLY 2.6 28.6 - - - +
54B PRO* 3.0 1.4 - - - +
55B HIS* 3.0 34.8 + - + +
56B GLU 4.3 4.4 - - - +
57B ILE* 3.7 29.4 - - + +
58B ARG* 5.0 6.9 + - - +
63B ARG* 3.4 27.7 - - - +
70B LEU* 3.3 20.6 - - + +
72B ASN* 5.3 3.9 - - - +
118B SER* 1.3 71.9 - - - +
120B ILE* 1.3 54.9 + - - +
121B ASP* 3.0 30.1 - - - +
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Residues in contact with ILE 120 (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 VAL* 5.5 2.7 - - + -
52B TYR 3.9 4.7 - - - +
53B GLY 4.1 0.2 - - - -
54B PRO* 4.0 22.9 - - + -
69B ALA* 4.3 22.2 - - + -
70B LEU 2.9 11.0 + - - +
71B VAL* 3.6 10.6 - - + +
72B ASN 3.0 22.9 + - - -
110B ILE* 4.2 31.6 - - + -
112B THR* 5.0 2.2 - - + -
115B HIS* 4.8 7.6 - - + -
119B GLN* 1.3 74.4 - - - +
121B ASP* 1.3 62.3 + - - +
122B ILE* 3.6 21.7 + - + -
145B VAL* 6.0 0.9 - - + -
150B ILE* 4.1 27.4 - - + -
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Residues in contact with ASP 121 (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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50B VAL 3.7 0.7 - - - +
51B VAL* 3.2 4.9 - - - -
52B TYR* 2.9 46.6 + - + +
55B HIS* 3.0 25.2 + - - -
72B ASN* 3.4 27.0 + - - +
119B GLN* 3.0 22.4 - - - +
120B ILE* 1.3 71.5 - - - +
122B ILE* 1.3 62.6 + - - +
123B TYR* 3.8 32.1 + - + +
91E PRO* 4.2 7.3 - - - +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL 3.4 6.7 - - - +
51B VAL* 3.9 15.5 - - + -
71B VAL* 4.2 20.6 - - + -
72B ASN 2.9 7.6 + - - +
73B CYS* 3.1 19.9 - - + -
74B GLN 2.9 22.2 + - - -
102B LEU* 5.4 1.1 - - + -
106B PHE* 4.1 32.8 - - + -
110B ILE* 5.9 2.0 - - + -
120B ILE* 3.6 15.7 + - + +
121B ASP* 1.3 76.7 - - - +
123B TYR* 1.3 71.3 + - - +
124B VAL* 4.4 9.9 - - + -
141B ALA* 4.2 22.2 - - + -
145B VAL* 4.8 8.5 - - + -
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Residues in contact with TYR 123 (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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48B LEU 3.9 0.6 - - - +
49B ALA* 3.3 4.9 - - - +
50B VAL* 2.9 36.4 + - + +
52B TYR* 3.7 36.3 - + - -
72B ASN* 5.1 7.9 + - - -
74B GLN* 3.1 40.4 - - + -
121B ASP* 3.8 27.5 - - + +
122B ILE* 1.3 81.9 - - - +
124B VAL* 1.3 65.8 - - - +
86E SER* 5.7 0.2 - - - +
87E ALA* 3.6 23.3 - - + -
88E SER* 3.8 19.5 - - - +
91E PRO* 3.6 28.6 + - + +
93E PHE 4.4 1.3 + - - -
94E GLU* 4.6 8.8 + - + -
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Residues in contact with VAL 124 (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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47B ALA* 5.1 0.2 - - + -
48B LEU 3.4 10.8 - - - +
49B ALA* 4.7 4.0 - - + -
74B GLN 2.9 12.4 + - - +
75B TYR* 3.5 9.5 - - + -
76B SER* 2.9 29.5 + - - -
102B LEU* 4.0 24.5 - - + -
122B ILE* 4.4 11.7 - - + -
123B TYR* 1.3 80.8 - - - +
125B GLN* 1.3 66.3 + - - +
126B VAL* 4.6 0.2 - - + -
137B CYS* 3.3 41.7 - - + +
141B ALA* 4.5 12.8 - - + -
88E SER* 5.6 0.9 - - - -
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Residues in contact with GLN 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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47B ALA* 3.6 1.2 - - - -
48B LEU* 2.9 44.7 + - + +
76B SER* 2.5 39.6 + - - -
78B ALA* 3.2 38.2 - - - +
124B VAL* 1.3 74.6 - - - +
126B VAL* 1.3 61.9 - - - +
127B LEU* 3.8 9.0 + - + +
84E ASP* 3.5 14.4 + - - +
86E SER* 3.7 22.0 + - - +
88E SER* 5.1 4.5 + - - +
140E LEU* 4.1 24.8 - - + +
142E LEU* 5.3 5.2 - - + -
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Residues in contact with VAL 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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45B THR* 4.9 4.7 - - + -
46B LYS 3.8 5.6 - - - +
47B ALA* 4.5 2.5 - - + +
75B TYR* 3.9 14.4 - - + +
76B SER 2.9 18.5 + - - +
77B SER* 4.2 9.0 - - - +
78B ALA* 3.1 24.7 + - - +
81B SER* 4.0 2.8 - - - -
124B VAL* 4.6 0.2 - - + -
125B GLN* 1.3 74.3 - - - +
127B LEU* 1.3 64.4 + - - +
128B GLN 3.7 23.8 - - - +
129B ALA* 4.4 4.5 - - + -
133B THR* 4.0 19.5 - - + -
137B CYS* 3.2 35.0 - - - -
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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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39B TYR* 4.4 9.9 - - + -
46B LYS* 2.9 25.4 + - + +
48B LEU* 4.5 11.7 - - + -
78B ALA* 4.5 3.3 - - - +
80B PHE* 3.4 26.8 - - + +
81B SER* 3.5 12.7 - - - -
125B GLN* 4.3 14.4 - - + +
126B VAL* 1.3 73.7 - - - +
128B GLN* 1.3 61.1 + - + +
41E VAL* 6.2 1.6 - - + -
42E VAL* 4.6 7.7 - - + +
59E LEU* 3.7 17.0 - - + -
140E LEU* 3.2 35.2 - - + -
142E LEU* 5.6 3.4 - - + -
289E PHE* 3.8 32.8 - - + -
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Residues in contact with GLN 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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44B ASN* 3.1 33.7 + - + +
45B THR* 3.2 9.7 - - - +
46B LYS* 2.6 62.3 + - + +
81B SER* 4.3 5.2 - - - +
126B VAL* 3.5 6.9 - - - +
127B LEU* 1.3 81.3 - - - +
129B ALA* 1.3 61.4 + - - +
42E VAL* 3.9 19.6 - - + +
43E SER* 3.9 12.5 + - - -
44E ASN* 3.2 43.6 + - - +
20K VAL* 5.1 1.4 + - - +
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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