Contacts of the strand formed by residues 155 - 163 (chain B) in PDB entry 3G4C
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 TYR 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.5 13.2 - - - +
7B ASP* 2.6 24.0 + - - -
8B LYS* 3.3 21.8 + - + -
9B GLY* 3.5 25.2 + - - -
67B LYS* 3.9 23.6 - - + -
68B ALA* 3.4 22.0 - - - -
69B PRO* 3.6 18.4 - - + -
87B LEU* 5.8 1.6 - - - +
94B LEU* 5.2 6.1 - - - +
97B GLU* 2.9 26.4 + - + +
98B PHE 3.5 20.2 - - - -
99B TYR* 3.4 27.2 - - + +
153B ASN 3.5 0.8 + - - -
154B LEU* 1.3 88.4 - - - +
156B THR* 1.3 58.4 + - - +
186B TYR* 3.9 0.4 - - - -
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Residues in contact with THR 156 (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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67B LYS* 3.3 5.0 - - - +
68B ALA 2.8 42.5 + - - +
70B ILE* 4.1 18.6 - - + -
73B ALA* 3.9 20.9 - - + -
86B GLU* 2.7 37.2 + - - +
87B LEU* 4.1 13.2 + - - +
94B LEU* 6.4 1.3 - - - -
154B LEU* 6.3 0.2 - - - -
155B TYR* 1.3 74.7 - - - +
157B ARG* 1.3 71.0 + - - +
158B PHE* 4.6 6.2 - - + -
74C ARG* 4.8 1.0 + - - -
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Residues in contact with ARG 157 (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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28A ARG 5.0 2.2 + - - -
29A VAL* 2.8 37.3 + - + +
30A SER 5.2 0.2 - - - -
10B PHE* 4.3 8.5 - - - -
65B HIS* 2.9 36.9 + - - +
66B VAL 3.2 6.7 - - - +
67B LYS* 3.8 30.7 - - + +
86B GLU* 3.5 1.9 - - - +
87B LEU* 2.8 64.4 + - + +
155B TYR 5.9 0.2 - - - -
156B THR* 1.3 82.9 + - - +
158B PHE* 1.3 65.8 + - - +
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Residues in contact with PHE 158 (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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29A VAL* 4.1 2.9 - - - +
64B PHE 3.9 0.3 - - - +
65B HIS* 3.5 2.8 - - - -
66B VAL* 2.9 70.5 + - + -
68B ALA* 4.4 9.2 - - + -
73B ALA* 4.3 13.2 - - + -
76B TRP* 3.8 28.3 - + - -
77B PHE* 3.7 30.3 - + + -
84B TYR* 4.2 3.6 - + - -
85B ASN 3.1 14.4 - - - +
86B GLU* 3.6 13.9 - - + -
156B THR* 4.6 10.5 - - + -
157B ARG* 1.3 81.5 - - - +
159B PHE* 1.3 75.8 + - - +
160B TRP* 4.1 15.3 - - + -
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Residues in contact with PHE 159 (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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22A SER 5.2 1.8 - - - -
25A ARG* 4.0 22.4 - - + -
26A ALA* 4.1 15.5 - - + -
29A VAL* 3.8 25.6 - - + -
30A SER 3.5 23.1 - - - -
59A HIS* 4.0 18.2 - + + +
14B VAL* 3.7 29.8 - - + -
63B THR* 3.8 16.8 - - + -
64B PHE 3.3 3.8 - - - -
65B HIS* 3.6 32.3 - + + -
84B TYR* 3.2 6.9 - - - -
85B ASN* 2.8 34.2 + - + +
158B PHE* 1.3 77.8 - - - +
160B TRP* 1.3 59.0 + - - +
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Residues in contact with TRP 160 (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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62B PHE 3.6 1.4 - - - +
63B THR* 3.2 2.5 - - - -
64B PHE* 2.8 64.6 + + + +
66B VAL* 5.0 0.4 - - + -
76B TRP* 3.3 41.5 - + - -
79B HIS* 5.1 3.6 - - + -
82B ALA* 3.3 13.5 - - + +
83B SER 3.3 7.6 - - - -
84B TYR* 3.1 43.4 + + - -
158B PHE* 4.1 12.6 - + + -
159B PHE* 1.3 76.4 - - - +
161B THR* 1.3 61.7 + - - +
162B VAL* 3.8 23.1 - - + -
166B SER* 5.6 0.4 - - - -
167B LEU* 3.6 32.5 - - + -
170B PHE* 3.7 26.5 - + + -
190B ILE* 3.8 11.2 - - + -
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Residues in contact with THR 161 (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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17A MET* 4.0 11.7 - - + -
58A GLU 4.1 15.7 - - - +
59A HIS* 2.6 32.3 + - - +
61A VAL* 4.4 2.9 - - + -
61B VAL* 3.8 18.6 - - + -
62B PHE 3.2 8.3 - - - +
63B THR* 2.8 20.8 + - - +
82B ALA* 3.4 4.2 - - - +
83B SER* 2.8 43.9 + - - +
160B TRP* 1.3 68.6 - - - +
162B VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 162 (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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61B VAL* 4.2 3.6 - - - -
62B PHE* 2.9 30.8 + - - +
64B PHE* 4.1 15.9 - - + -
81B ILE 4.0 4.7 - - - +
82B ALA* 4.2 3.8 - - + +
160B TRP* 3.8 49.8 - - + +
161B THR* 1.3 77.6 - - - +
163B ASN* 1.3 64.7 + - - +
166B SER* 3.5 29.6 - - - +
167B LEU* 3.7 18.6 - - + +
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Residues in contact with ASN 163 (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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83A SER* 4.4 2.4 + - - -
58B GLU* 3.4 28.2 + - - +
60B ILE 3.1 13.7 - - - +
61B VAL* 4.0 9.6 - - + +
62B PHE* 4.9 0.7 - - - -
81B ILE* 4.9 3.2 + - - +
162B VAL* 1.3 77.5 - - - +
164B ALA* 1.3 65.4 + - - +
165B ARG* 3.0 19.9 + - - +
166B SER* 3.0 14.5 + - - -
167B LEU* 2.9 21.3 + - - +
300D FAD 2.8 33.0 + - - -
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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