Contacts of the strand formed by residues 64 - 71 (chain B) in PDB entry 3SHD
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 HIS 64 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B PRO 3.8 0.6 - - - -
63B GLN* 1.3 107.4 + - + +
65B PHE* 1.3 61.6 + - - +
84B PHE* 3.2 4.5 - - - +
85B ALA* 2.7 41.1 + - + +
135B ARG* 3.4 64.0 + - + -
136B TYR 3.6 18.4 - - - +
137B PRO* 5.0 4.3 - - + -
138B LEU* 3.8 9.2 - - - +
67C ARG* 5.1 11.3 + - - -
125C GLU* 3.8 8.0 + - - -
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Residues in contact with PHE 65 (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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64B HIS* 1.3 71.6 - - - +
66B ILE* 1.3 60.0 + - - +
67B ARG* 3.2 41.5 - - - -
68B MET* 3.6 13.7 - - + -
82B PHE* 3.6 22.2 - + + -
83B LEU 3.3 12.3 - - - -
84B PHE* 4.0 11.4 - + + -
135B ARG* 3.4 0.9 - - - -
136B TYR* 2.6 48.4 + + - +
137B PRO 4.1 11.0 - - - +
138B LEU* 3.8 9.7 - - - +
140B MET* 4.1 25.1 - - + -
141B ILE* 3.7 34.1 - - + -
65L PHE* 5.8 0.4 - + - -
140L MET* 4.4 10.1 - - + -
141L ILE* 5.4 2.7 - - + -
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Residues in contact with ILE 66 (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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11B VAL* 3.7 30.7 - - + -
64B HIS 3.4 1.0 + - - -
65B PHE* 1.3 72.8 - - - +
67B ARG* 1.3 73.5 + - + +
83B LEU* 2.8 25.0 + - + +
84B PHE 3.9 4.5 - - - +
85B ALA* 3.8 28.0 - - + -
129B CYS* 3.8 23.6 - - + -
130B TYR* 4.2 18.2 - - + -
134B GLN* 3.2 35.9 - - + +
135B ARG* 4.3 5.4 - - + +
136B TYR* 3.4 12.8 - - - -
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Residues in contact with ARG 67 (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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65B PHE* 3.2 21.4 - - - -
66B ILE* 1.3 94.8 - - + +
68B MET* 1.3 80.0 + - - +
69B HIS* 3.7 35.2 + - - -
83B LEU* 2.7 36.8 + - + +
125B GLU* 5.8 0.2 + - - -
129B CYS* 3.9 12.2 - - - -
134B GLN* 3.7 17.3 - - - +
64H HIS* 4.7 7.1 + - - -
135H ARG* 5.3 0.2 - - - +
139L GLU* 3.1 32.4 + - - +
140L MET* 3.7 15.9 + - + +
142L GLY* 3.1 37.2 + - - +
143L ASP 4.4 3.6 + - - -
144L PHE* 6.3 0.2 - - - -
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Residues in contact with MET 68 (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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65B PHE* 3.8 12.6 - - + -
67B ARG* 1.3 103.4 + - - +
69B HIS* 1.3 64.5 + - - +
70B GLN* 3.7 27.6 - - + +
80B LEU* 3.9 10.8 - - + -
81B ARG 3.4 21.1 - - - +
82B PHE* 3.8 33.0 - - + -
44L LEU* 4.2 7.9 - - + -
82L PHE* 3.9 15.9 - - - -
140L MET 3.1 16.1 + - - +
141L ILE* 3.0 45.9 - - + +
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Residues in contact with HIS 69 (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 ARG* 3.7 31.0 + - - -
68B MET* 1.3 79.0 + - - +
70B GLN* 1.3 60.3 + - - +
71B TRP* 3.9 2.1 + - - +
79B PHE 3.9 0.9 - - - +
80B LEU* 3.7 0.3 - - - -
81B ARG* 2.9 45.6 + - + +
83B LEU* 4.5 18.2 - - + +
122B LEU* 3.7 36.2 - - + +
125B GLU* 3.6 22.7 - - + +
126B SER* 4.8 2.2 - - - -
129B CYS* 3.6 26.4 - - - -
142L GLY 3.9 1.8 - - - -
144L PHE* 3.9 20.8 - + + -
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Residues in contact with GLN 70 (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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68B MET* 3.7 10.4 - - + +
69B HIS* 1.3 71.3 - - - +
71B TRP* 1.3 65.6 + - - +
72B ILE* 5.9 0.7 - - + -
79B PHE 3.3 6.3 - - - +
80B LEU* 3.5 29.5 - - + +
38L LEU* 4.3 13.7 - - - +
42L GLU 2.8 24.3 + - - -
43L THR* 3.4 22.5 + - - +
44L LEU* 3.4 15.3 + - - +
141L ILE 4.4 1.8 - - - +
142L GLY 3.2 12.8 + - - +
143L ASP* 3.5 10.0 + - - +
144L PHE* 3.1 25.6 + - - +
146L TRP* 4.0 16.9 - - + -
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Residues in contact with TRP 71 (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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69B HIS 4.7 2.5 - - - +
70B GLN* 1.3 78.0 - - - +
72B ILE* 1.3 75.9 + - - +
73B ALA* 3.3 41.4 - - + +
74B PRO* 4.1 10.1 - - + -
79B PHE* 2.8 62.6 + + + +
81B ARG* 6.1 0.9 - - - -
119B ARG 5.8 0.4 - - - -
120B SER* 4.1 21.8 - - - -
121B PRO* 3.9 25.4 - - + +
122B LEU* 3.9 28.7 - - + -
158B SO4 5.9 2.9 - - - -
144L PHE* 3.5 35.3 - + + +
145L ASN* 4.8 8.3 + - + +
146L TRP* 4.9 2.5 - - - -
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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