Contacts of the strand formed by residues 64 - 71 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ARG* 4.7 6.1 + - - -
125A GLU* 4.2 3.4 - - - -
134A GLN* 5.8 0.4 + - - -
139I GLU* 2.8 28.6 + - - -
62K PRO 3.8 0.2 - - - -
63K GLN* 1.3 104.0 + - + +
65K PHE* 1.3 58.5 - - - +
84K PHE* 3.3 8.8 - - - -
85K ALA* 2.8 39.2 + - + +
87K GLU* 6.2 0.4 - - - +
135K ARG* 3.1 71.8 + - + +
136K TYR 3.4 18.4 - - - +
137K PRO* 4.9 1.6 - - + -
138K LEU* 3.8 8.3 - - - -
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Residues in contact with PHE 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F PHE* 5.4 0.7 - + - -
140F MET* 3.6 34.5 - - + -
141F ILE* 4.7 3.4 - - + -
64K HIS* 1.3 73.4 - - - +
66K ILE* 1.3 60.9 + - - +
67K ARG 3.4 32.1 - - - -
68K MET* 3.7 11.9 - - + -
82K PHE* 3.7 24.2 - + + -
83K LEU 3.7 9.0 - - - -
84K PHE* 3.7 26.5 - + + -
135K ARG* 3.5 0.3 - - - -
136K TYR* 2.6 45.5 + - + +
137K PRO 4.1 10.8 - - - +
138K LEU* 4.0 1.7 - - + +
140K MET* 3.8 22.2 - - + -
141K ILE* 4.0 16.4 - - + -
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Residues in contact with ILE 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F MET* 4.5 1.0 - - - +
11K VAL* 4.5 9.0 - - + -
64K HIS 4.7 0.2 - - - -
65K PHE* 1.3 79.9 - - - +
67K ARG* 1.3 63.3 + - + +
83K LEU* 2.9 25.8 + - + +
84K PHE 3.3 31.4 - - - +
85K ALA* 3.4 21.8 - - + +
129K CYS* 3.9 27.8 - - + -
130K TYR* 4.4 14.1 - - + +
134K GLN* 2.7 46.5 - - - +
135K ARG* 4.9 3.6 - - + -
136K TYR* 3.7 15.4 - - - -
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Residues in contact with ARG 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F GLU* 3.0 34.2 + - - +
140F MET* 3.4 17.0 - - - +
142F GLY* 3.0 29.9 + - - +
143F ASP 3.7 7.5 + - - -
144F PHE* 4.7 3.0 - - - +
65K PHE* 3.4 12.9 - - - -
66K ILE* 1.3 92.0 - - + +
68K MET* 1.3 77.0 + - - +
69K HIS* 3.4 44.2 + - + +
83K LEU* 2.9 31.6 + - + +
125K GLU* 5.9 0.2 + - - -
129K CYS* 4.2 15.3 - - - -
134K GLN* 4.3 5.6 - - - +
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Residues in contact with MET 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 4.3 3.8 - - + -
82F PHE* 3.9 13.2 - - - -
140F MET 2.9 5.9 + - - -
141F ILE* 3.4 49.4 - - + +
65K PHE* 4.0 1.3 - - + -
67K ARG* 1.3 93.7 + - - +
69K HIS* 1.3 86.6 + - - +
70K GLN* 3.6 7.0 - - + +
80K LEU* 3.7 28.7 - - + -
81K ARG 3.2 14.8 - - - +
82K PHE* 3.3 47.3 - - + -
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Residues in contact with HIS 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F GLY 3.8 0.7 - - - -
144F PHE* 3.8 23.0 - + + -
67K ARG* 3.4 50.8 + - + +
68K MET* 1.3 76.2 - - - +
70K GLN* 1.3 61.0 - - - +
71K TRP* 3.8 1.3 + - - +
79K PHE 3.6 2.4 - - - +
81K ARG* 2.8 44.6 + - + +
83K LEU* 4.7 13.4 - - + +
122K LEU* 4.2 26.8 - - + +
125K GLU* 4.2 21.9 + - + +
126K SER* 4.9 3.9 + - - -
129K CYS* 3.7 19.5 - - - -
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Residues in contact with GLN 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F LEU* 4.1 15.2 - - - +
42F GLU 3.2 21.3 + - - -
43F THR* 3.5 7.8 + - - -
44F LEU* 3.2 29.9 + - - +
141F ILE 4.5 1.5 - - - +
142F GLY 3.1 10.7 + - - +
143F ASP* 3.0 16.3 + - - +
144F PHE 2.7 31.9 + - - -
146F TRP* 3.9 24.5 - - + -
2K PHE* 5.8 3.6 - - - -
4K PRO* 6.0 1.0 - - - +
68K MET* 3.6 9.2 - - + +
69K HIS* 1.3 72.9 - - - +
71K TRP* 1.3 59.9 + - - +
78K PRO* 6.3 1.2 - - - +
79K PHE 3.4 4.0 - - - +
80K LEU* 3.4 28.1 - - + +
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Residues in contact with TRP 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F PHE* 3.5 32.4 - + + -
145F ASN* 4.7 7.2 - - + +
146F TRP* 4.5 4.3 - - - -
69K HIS* 3.8 2.9 + - + +
70K GLN* 1.3 77.9 - - - +
72K ILE* 1.3 74.3 + - - +
73K ALA* 3.6 36.8 - - + +
74K PRO* 3.9 12.8 - - + -
78K PRO* 3.6 0.5 - - - +
79K PHE* 2.6 66.3 + + + +
120K SER* 3.9 28.0 - - - -
121K PRO* 4.2 20.3 - - + +
122K LEU* 3.7 33.6 - - + +
158K SO4 5.9 2.0 - - - -
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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