Contacts of the strand formed by residues 189 - 197 (chain A) in PDB entry 2F1Y
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 VAL 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A THR* 3.4 1.1 - - - -
75A VAL 2.8 31.1 + - - -
78A PHE* 3.4 43.5 - - + -
140A ILE* 3.9 19.1 - - + -
176A VAL* 4.0 13.5 - - + -
183A PHE 3.6 20.6 - - - +
184A ILE* 3.9 10.1 - - + -
188A LYS* 1.3 76.8 - - - +
190A THR* 1.3 64.1 + - - +
191A PHE* 3.6 28.9 - - + -
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Residues in contact with THR 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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72A GLN* 4.0 30.1 - - + +
73A PHE 3.7 3.4 - - - +
74A THR* 3.0 27.7 + - - +
140A ILE* 3.6 5.2 - - - +
141A ILE* 3.0 44.5 + - + +
183A PHE 4.6 2.4 + - - -
188A LYS* 4.3 1.6 + - - +
189A VAL* 1.3 75.4 - - - +
191A PHE* 1.3 72.2 + - - +
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Residues in contact with PHE 191 (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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72A GLN* 3.1 5.0 - - - +
73A PHE* 2.7 47.4 + + - +
75A VAL* 3.8 21.5 - - + -
78A PHE* 3.9 9.9 - + - -
99A ILE* 3.9 11.7 - - + +
101A VAL* 3.5 37.7 - - + -
115A VAL* 4.0 13.5 - - + -
117A PHE* 3.7 35.2 - + + -
139A LYS 3.4 4.3 - - - -
140A ILE* 3.8 22.2 - - + -
189A VAL* 3.6 29.6 - - + -
190A THR* 1.3 76.0 - - - +
192A GLU* 1.3 61.2 + - - +
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Residues in contact with GLU 192 (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 THR* 3.5 28.1 - - + +
71A PHE 3.4 11.0 - - - +
72A GLN* 3.2 29.7 + - + +
99A ILE* 4.3 0.2 - - - -
117A PHE* 3.7 0.9 - - - -
137A VAL 3.6 1.7 - - - +
139A LYS* 2.7 67.6 + - + +
141A ILE* 3.6 19.9 - - + +
190A THR 4.2 0.2 + - - -
191A PHE* 1.3 76.7 - - - +
193A VAL* 1.3 74.1 + - - +
194A PHE* 5.2 3.8 + - - +
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Residues in contact with VAL 193 (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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69A ALA 3.6 1.6 - - - +
70A THR* 3.2 3.0 - - - +
71A PHE* 2.9 56.1 + - + -
99A ILE* 3.6 23.1 - - + -
117A PHE* 4.0 14.6 - - + -
119A LEU* 4.0 29.8 - - + -
136A ALA* 4.4 1.8 - - + -
137A VAL 3.4 4.5 - - - +
138A LEU* 4.1 13.2 - - + -
192A GLU* 1.3 82.8 - - - +
194A PHE* 1.3 73.7 + - - +
195A VAL* 4.0 2.7 - - + +
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Residues in contact with PHE 194 (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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68A GLU* 3.9 31.9 - - + -
69A ALA* 3.4 9.2 - - - -
70A THR* 3.3 25.1 - - + +
136A ALA* 3.0 7.5 - - - +
137A VAL* 2.9 53.9 + - + +
192A GLU* 5.2 4.6 + - - +
193A VAL* 1.3 73.9 - - - +
195A VAL* 1.3 57.9 + - - +
196A GLN* 3.5 43.5 - - + -
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Residues in contact with VAL 195 (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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67A SER 4.1 0.2 - - - +
68A GLU* 3.0 6.1 - - - +
69A ALA 2.9 39.4 + - - +
71A PHE* 4.4 17.5 - - + -
92A VAL* 4.0 23.7 - - + +
97A TRP* 4.1 27.1 - - + -
119A LEU* 4.2 7.0 - - + -
134A ALA* 4.0 23.8 - - + -
135A GLN 3.6 3.8 - - - +
136A ALA* 4.0 2.0 - - + -
193A VAL* 4.1 9.4 - - + -
194A PHE* 1.3 75.4 - - - +
196A GLN* 1.3 71.1 + - - +
197A ALA* 4.2 1.3 - - + +
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Residues in contact with GLN 196 (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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67A SER 3.4 5.6 - - - +
68A GLU* 3.4 21.7 + - + +
133A HIS 3.8 0.5 - - - +
134A ALA* 3.2 6.1 - - - +
135A GLN* 2.9 50.7 + - + +
194A PHE* 3.5 37.7 - - + -
195A VAL* 1.3 75.1 - - - +
197A ALA* 1.3 60.1 + - - +
199A LEU* 3.6 32.1 - - + +
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Residues in contact with ALA 197 (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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67A SER* 2.8 19.8 + - - +
92A VAL* 3.9 21.1 - - + -
93A ARG* 3.8 21.0 - - + +
97A TRP* 4.1 22.7 - - + -
132A CYS* 4.9 2.9 - - + -
133A HIS 3.6 4.0 - - - +
134A ALA* 4.5 1.6 - - + +
195A VAL* 4.2 0.8 - - + -
196A GLN* 1.3 72.3 - - - +
198A ASP* 1.3 76.7 + - - +
199A LEU* 3.3 9.5 + - - +
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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