Contacts of the strand formed by residues 184 - 190 (chain A) in PDB entry 3DRW
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A PRO* 5.1 8.1 - - - -
164A GLU* 3.7 3.3 - - - +
165A PHE* 3.0 47.7 + - - +
183A SER* 1.3 76.6 - - - +
185A ARG* 1.3 61.0 + - - +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 5.5 2.8 - - - +
69A PRO* 3.2 32.5 - - + +
70A ALA 3.4 3.6 + - - +
162A ILE* 3.6 34.9 - - + +
163A PHE 3.2 6.7 - - - +
164A GLU* 3.2 32.8 + - + +
165A PHE* 3.4 6.8 - - - -
184A GLY* 1.3 74.8 - - - +
186A PHE* 1.3 57.9 + - - +
187A ILE* 4.2 21.7 - - + +
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Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.7 1.6 - - + -
56A PHE* 3.7 25.1 - + - -
59A ARG* 3.6 31.9 - - + -
60A LEU* 3.8 27.6 - - + -
63A THR* 3.5 30.1 - - + -
70A ALA* 3.4 11.9 - - + +
72A VAL* 3.6 32.8 - - + -
163A PHE* 2.8 50.6 + + + +
165A PHE* 3.7 1.3 - - + -
185A ARG* 1.3 73.2 - - - +
187A ILE* 1.3 58.6 + - - +
188A VAL* 3.5 26.9 - - + -
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Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA 2.8 17.4 + - - +
71A ALA* 3.2 13.9 - - + +
72A VAL* 2.8 28.8 + - - +
160A ASN* 5.5 3.4 - - + -
161A ARG 3.5 4.3 - - - +
162A ILE* 3.3 33.9 - - + -
185A ARG* 4.2 25.8 - - + +
186A PHE* 1.3 78.1 - - - +
188A VAL* 1.3 68.6 + - - +
189A SER* 4.0 17.6 + - - +
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.9 14.4 - - + -
56A PHE* 3.8 19.7 - - + -
72A VAL 3.2 10.8 - - - +
74A LEU* 3.7 28.0 - - + -
83A PHE* 4.2 14.1 - - + -
159A ILE 4.3 1.9 - - - +
160A ASN* 3.7 1.4 - - - -
161A ARG* 2.9 41.5 + - + +
163A PHE* 4.1 9.6 - - + -
186A PHE* 3.5 31.2 - - + -
187A ILE* 1.3 74.9 - - - +
189A SER* 1.3 58.3 + - - +
190A ALA 3.9 0.2 + - - -
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Residues in contact with SER 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ALA* 5.2 5.9 - - - +
72A VAL 3.4 6.9 + - - -
73A PRO* 3.4 5.9 - - - +
74A LEU* 2.7 32.8 + - - -
160A ASN* 3.4 12.0 - - - +
187A ILE* 3.9 15.4 + - - +
188A VAL* 1.3 73.2 - - - +
190A ALA* 1.3 59.5 + - - +
191A ARG* 3.4 37.1 + - - +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 4.1 7.2 - - + -
158A LYS* 3.7 25.9 - - + -
159A ILE 3.5 23.7 + - - +
160A ASN* 2.9 10.1 - - - +
189A SER* 1.3 68.4 - - - +
191A ARG* 1.3 78.4 + - - +
192A PHE* 3.6 25.6 - - + -
195A ILE* 3.7 12.0 - - + +
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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