Contacts of the strand formed by residues 116 - 124 (chain D) in PDB entry 5FL6
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 ALA 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D LEU* 6.0 0.2 - - + -
96D HIS 3.1 15.9 - - - +
97D TRP* 3.9 11.7 - - + -
105D SER* 3.7 12.7 - - - +
114D PHE* 3.3 1.6 + - - +
115D PRO* 1.3 80.6 - - - +
117D GLU* 1.3 64.5 + - - +
146D PHE* 3.7 3.6 - - - -
147D LEU* 2.9 38.4 + - + +
224D LEU* 4.4 6.3 - - + -
227D LEU* 4.0 17.3 - - + -
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D LEU* 3.4 8.6 - - - +
96D HIS* 2.8 38.3 + - + +
105D SER* 3.5 12.0 - - - -
106D GLU* 2.7 31.3 + - - +
107D HIS* 2.8 31.2 + - - -
116D ALA* 1.3 77.0 - - - +
118D ILE* 1.3 61.3 + - - +
119D HIS* 2.8 31.6 + - + +
144D ALA* 3.8 5.7 - - - +
145D ALA 3.3 22.2 - - - +
146D PHE* 3.7 11.4 - - + -
147D LEU* 4.4 2.5 - - - -
212D VAL* 6.1 0.4 - - - -
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 4.2 17.9 - - + -
94D HIS 3.6 11.0 - - - +
95D LEU* 3.5 17.9 - - + -
117D GLU* 1.3 72.7 - - - +
119D HIS* 1.3 74.6 + - - +
120D VAL* 4.3 12.8 - - + -
143D LEU 3.6 0.7 - - - +
144D ALA* 3.2 6.4 - - - -
145D ALA* 2.9 56.1 + - + +
147D LEU* 4.1 4.6 - - + +
157D TYR* 3.4 26.7 - - + +
184D LEU* 3.9 25.6 - - + +
185D LEU* 4.1 6.5 - - + -
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Residues in contact with HIS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 3.1 6.2 - - - +
94D HIS* 3.0 46.0 + - + +
96D HIS* 3.3 11.3 + + - -
106D GLU* 3.2 22.2 - - + -
107D HIS* 4.6 0.4 + + - -
117D GLU* 2.8 30.6 + - + +
118D ILE* 1.3 86.0 - - - +
120D VAL* 1.3 62.8 + - - +
121D VAL 4.0 1.0 + - - -
142D VAL* 3.7 12.6 - - + -
143D LEU 3.3 2.9 - - - -
144D ALA* 3.7 5.4 - - + -
210D TRP* 3.5 25.9 - + - -
266D Y0R 3.3 2.0 + - - -
1260D ZN 2.1 35.7 - - - -
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PHE* 4.5 11.2 - - + -
74D LEU* 4.1 19.1 - - + -
90D ALA* 4.5 2.9 - - + -
92D GLN 3.6 8.5 - - - +
93D LEU* 3.9 16.2 - - + -
118D ILE* 4.3 8.1 - - + -
119D HIS* 1.3 75.2 - - - +
121D VAL* 1.3 61.4 + - - +
122D HIS* 3.0 31.1 + - + +
142D VAL* 3.4 1.7 - - - +
143D LEU* 2.8 42.0 + - + +
181D ILE* 5.2 2.5 - - + -
184D LEU* 6.4 0.2 - - + -
185D LEU* 4.1 30.7 - - + -
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ALA* 3.6 2.4 - - - +
91D LEU* 2.7 43.8 + - + +
92D GLN* 2.8 27.7 + - + +
94D HIS* 3.7 31.0 - - + -
119D HIS 4.6 0.2 - - - +
120D VAL* 1.3 74.5 - - - +
122D HIS* 1.3 61.7 + - - +
140D LEU* 5.1 11.7 - - + -
141D ALA 3.8 2.7 - - - -
142D VAL* 4.3 15.9 - - + +
199D LEU* 5.5 0.7 - - + -
266D Y0R 3.7 36.1 - - - +
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Residues in contact with HIS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PHE* 3.9 8.5 - + - -
80D MET* 3.5 37.2 - - + +
88D TYR* 3.7 16.2 - - + -
89D ARG 3.1 8.1 - - - +
90D ALA* 3.4 32.3 - - + +
91D LEU* 4.3 3.4 - - - +
120D VAL* 3.0 45.1 + - + -
121D VAL* 1.3 72.8 - - - +
123D LEU* 1.3 59.1 + - - +
140D LEU* 3.2 14.4 - - - +
141D ALA 2.8 39.5 + - - +
143D LEU* 3.7 21.9 - - + +
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D TYR* 3.3 3.0 - - - -
89D ARG* 2.8 65.8 + - - +
91D LEU* 4.0 25.3 - - + +
122D HIS* 1.3 73.0 - - - +
124D SER* 1.3 71.9 + - - +
125D THR 3.4 0.2 + - - -
127D PHE* 3.6 13.9 - - + +
128D ALA 3.9 4.5 - - - +
129D ARG* 3.8 21.3 - - - +
130D VAL* 3.9 5.6 - - + +
133D ALA* 3.4 33.9 - - + -
139D GLY 3.6 4.3 - - - +
140D LEU* 3.8 7.4 - - + -
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Residues in contact with SER 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D GLU 3.7 4.4 + - - -
88D TYR* 3.3 16.1 - - - -
89D ARG* 3.0 9.8 + - - -
123D LEU* 1.3 74.0 - - - +
125D THR* 1.3 58.9 + - - +
126D ALA* 3.0 22.7 + - - +
127D PHE* 3.0 30.4 + - - +
138D GLY 3.5 17.3 - - - -
139D GLY* 2.9 21.9 + - - -
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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