Contacts of the strand formed by residues 154 - 159 (chain X) in PDB entry 3F6E
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 154 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92X LEU 2.9 14.9 + - - +
93X ILE* 3.8 10.3 - - + -
94X VAL* 2.9 31.2 + - - +
123X VAL* 4.1 4.0 - - - -
124X LYS* 4.1 4.7 - - + -
125X TRP* 3.4 21.1 - - + +
142X ALA* 3.5 36.1 - - + +
145X MET* 3.8 16.4 - - + -
146X ALA* 3.7 26.2 - - + +
152X GLY 4.1 0.4 - - - +
153X PRO* 1.4 80.6 - - - +
155X TYR* 1.3 62.8 + - - +
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Residues in contact with TYR 155 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X THR* 2.8 44.3 + - + +
82X LEU* 5.7 0.9 - - + -
94X VAL* 3.2 28.7 - - + -
96X ALA* 3.4 20.0 - - + +
112X ASN* 2.9 22.5 + - - -
115X ALA 3.6 22.9 - - - -
116X ALA* 4.7 2.2 - - - -
118X LEU* 4.2 0.7 - - + +
119X PRO* 3.5 26.7 - - + -
123X VAL* 4.2 5.4 - - + -
125X TRP* 3.0 12.8 + - - +
126X SER* 3.2 21.5 - - - +
127X TYR* 3.0 27.3 + - - +
142X ALA* 5.7 0.2 - - - -
154X VAL* 1.3 78.2 - - - +
156X LEU* 1.3 64.5 + - - +
157X SER* 4.3 13.7 - - - -
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Residues in contact with LEU 156 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X ILE* 5.9 0.7 - - + -
94X VAL 2.9 11.0 + - - +
95X THR* 3.2 11.8 - - + -
96X ALA 3.0 23.7 + - - +
125X TRP* 4.5 4.9 - - + -
127X TYR* 3.4 22.4 - - + +
129X PRO* 3.9 14.1 - - + -
135X VAL* 4.7 3.4 - - + +
138X ALA* 3.8 23.8 - - + -
139X MET* 3.8 51.6 - - + +
142X ALA* 4.8 10.1 - - + -
155X TYR* 1.3 79.1 - - - +
157X SER* 1.3 58.4 + - - +
158X VAL* 4.0 17.5 - - + +
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Residues in contact with SER 157 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96X ALA 3.3 8.3 + - - +
97X GLY 5.0 0.2 - - - -
98X GLN* 3.5 12.6 + - - +
112X ASN* 4.5 5.1 + - - -
115X ALA* 3.7 20.5 - - - +
127X TYR 2.9 12.1 + - - -
128X GLU* 2.7 32.2 + - - +
129X PRO* 3.0 25.5 - - - +
155X TYR* 4.3 12.3 - - - -
156X LEU* 1.3 73.8 - - - +
158X VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 158 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X THR* 5.6 4.0 - - - -
96X ALA 3.0 12.6 + - - +
97X GLY* 3.6 6.3 - - - -
98X GLN* 2.9 19.2 + - - -
129X PRO* 4.9 0.7 - - + -
135X VAL* 3.9 17.9 - - + -
139X MET* 5.4 1.1 - - + -
156X LEU* 4.0 28.3 - - + +
157X SER* 1.3 79.2 + - - +
159X PRO* 1.3 79.2 - - - +
160X TYR* 3.4 2.1 + - - -
162X ASP* 3.8 16.2 - - + +
163X TRP* 3.5 42.3 + - + -
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Residues in contact with PRO 159 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X GLN* 3.6 19.0 - - + -
99X GLN 3.3 18.2 - - - +
101X ARG* 3.6 35.2 - - + +
104X ILE* 4.2 1.8 - - + -
128X GLU* 4.1 14.6 - - + +
129X PRO* 4.9 1.3 - - + -
157X SER 3.9 6.1 - - - +
158X VAL* 1.3 88.5 - - - +
160X TYR* 1.3 66.6 + - - +
161X ASP* 3.1 13.2 - - - +
162X ASP* 3.0 36.9 + - - +
163X TRP* 4.2 0.3 + - - -
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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