Contacts of the strand formed by residues 86 - 97 (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 ARG 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D ALA 5.6 1.8 + - - -
45D LEU* 3.9 15.2 - - - +
81D ALA* 3.3 3.5 - - - -
82D LEU* 2.8 69.3 + - + +
83D GLY* 3.0 21.6 + - - +
84D PRO* 3.8 7.9 - - - +
85D GLY* 1.3 79.6 - - - +
87D GLU* 1.3 60.2 + - - +
88D TYR* 3.4 16.6 + - + +
194D GLN* 2.8 31.1 + - - -
209D ILE* 4.3 8.3 - - - +
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Residues in contact with GLU 87 (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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79D GLU* 5.8 2.9 - - - +
80D MET 3.7 3.4 - - - +
81D ALA* 3.4 24.9 + - - +
83D GLY 5.3 0.2 - - - -
85D GLY* 3.8 12.9 + - - -
86D ARG* 1.3 79.7 - - - +
88D TYR* 1.3 69.8 + - - +
124D SER* 3.7 4.3 + - - -
125D THR* 3.1 42.1 + - + +
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Residues in contact with TYR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLU* 3.5 6.9 - - - +
80D MET* 2.7 50.3 + - + +
82D LEU* 3.7 17.8 - - + +
86D ARG* 3.4 28.5 + - + +
87D GLU* 1.3 77.9 + - - +
89D ARG* 1.3 62.7 + - - +
122D HIS* 3.7 14.1 - - + -
123D LEU 3.3 7.6 - - - +
124D SER* 3.3 29.8 - - - -
125D THR* 4.2 8.7 - - - +
138D GLY* 2.7 37.6 + - - -
140D LEU 4.0 0.4 - - - -
141D ALA* 3.5 29.6 - - + -
209D ILE* 4.2 8.3 - - - +
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Residues in contact with ARG 89 (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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76A PRO* 3.6 33.2 - - - +
76D PRO* 6.5 0.4 - - + -
77D GLY 5.7 4.0 - - - +
78D LEU 3.2 15.0 - - - +
79D GLU* 4.9 3.8 - - + -
88D TYR* 1.3 74.3 - - - +
90D ALA* 1.3 68.2 + - - +
91D LEU* 3.6 4.8 + - + +
122D HIS* 3.1 5.9 - - - -
123D LEU* 2.8 55.6 + - + +
124D SER 3.0 26.9 + - - -
125D THR* 3.5 21.2 - - + +
127D PHE 2.9 19.6 + - - -
128D ALA* 3.4 21.4 + - - +
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Residues in contact with ALA 90 (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* 4.1 5.8 - - + -
74D LEU* 3.8 22.6 - - + +
75D PRO 4.1 14.9 - - - +
76D PRO* 5.6 1.0 - - - +
78D LEU* 2.9 29.7 + - + +
89D ARG* 1.3 78.1 - - - +
91D LEU* 1.3 62.9 + - - +
120D VAL* 4.5 0.7 - - + -
121D VAL 3.7 2.7 - - - +
122D HIS* 3.4 27.2 - - + +
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Residues in contact with LEU 91 (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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73D THR* 4.0 5.0 - - - +
74D LEU* 3.0 28.0 + - - +
89D ARG* 4.2 11.4 - - + +
90D ALA* 1.3 79.5 - - - +
92D GLN* 1.3 69.4 + - + +
121D VAL* 2.7 29.5 + - + +
122D HIS 4.5 0.9 - - - -
123D LEU* 4.0 32.8 - - + +
130D VAL* 3.3 33.0 - - + -
140D LEU* 4.8 1.1 - - + -
266D Y0R 5.3 3.6 - - - +
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Residues in contact with GLN 92 (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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71D GLN* 3.4 24.0 + - + +
72D LEU 3.2 16.4 - - - +
73D THR* 4.3 4.7 - - + +
74D LEU* 3.8 9.9 - - - +
91D LEU* 1.3 89.1 - - + +
93D LEU* 1.3 64.4 + - - +
94D HIS* 2.7 23.8 + - - -
120D VAL* 3.6 1.9 - - - +
121D VAL* 2.8 41.1 + - + +
266D Y0R 3.4 21.0 + - - +
1261D GOL 3.3 29.1 + - - -
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D VAL 5.7 0.4 - - - +
71D GLN* 3.3 1.4 - - - -
72D LEU* 2.7 68.3 + - + +
74D LEU* 4.2 6.5 - - + +
92D GLN* 1.3 78.8 - - - +
94D HIS* 1.3 67.5 + - - +
95D LEU* 5.4 5.4 - - + -
118D ILE* 4.2 14.8 - - + -
119D HIS 3.1 14.8 - - - +
120D VAL* 3.9 17.3 - - + -
160D LEU* 4.6 8.1 - - + -
181D ILE* 3.7 29.8 - - + -
184D LEU* 3.7 20.6 - - + -
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Residues in contact with HIS 94 (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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69D SER* 3.5 8.7 - - - +
70D VAL 3.1 17.9 - - - +
71D GLN* 3.9 4.5 - - - -
92D GLN* 2.7 25.9 + - - +
93D LEU* 1.3 77.9 - - - +
95D LEU* 1.3 67.7 + - - +
96D HIS* 3.4 11.0 - + - -
118D ILE* 3.6 4.5 - - - +
119D HIS* 3.0 34.1 + - + +
121D VAL* 3.7 13.0 - - + -
266D Y0R 3.1 22.8 + - - -
1260D ZN 2.2 31.6 - - - -
1261D GOL 3.3 29.7 + - - +
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Residues in contact with LEU 95 (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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69D SER* 2.6 25.2 + - - -
70D VAL* 3.5 14.7 + - + +
93D LEU* 5.4 4.3 - - + -
94D HIS* 1.3 81.5 - - - +
96D HIS* 1.3 70.1 + - - +
97D TRP* 3.4 16.1 - - + -
117D GLU 3.4 5.2 - - - +
118D ILE* 3.5 39.5 - - + +
147D LEU* 4.4 5.2 - - + -
157D TYR* 4.3 20.4 - - + -
160D LEU* 5.9 7.9 - - + -
161D LEU* 5.2 4.5 - - + -
164D LEU* 6.4 0.2 - - + -
227D LEU* 3.6 31.2 - - + -
242D ASN* 3.4 9.7 + - - -
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Residues in contact with HIS 96 (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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11D TYR* 3.5 19.5 - - - -
69D SER* 5.3 2.5 - - - -
94D HIS* 3.4 6.7 - + - -
95D LEU* 1.3 79.5 + - - +
97D TRP* 1.3 62.8 + - - +
104D GLY 3.5 8.7 - - - +
106D GLU* 3.3 28.7 + - + -
116D ALA* 3.1 5.9 - - - +
117D GLU* 2.8 38.8 + - + +
119D HIS* 3.3 20.2 - + - -
200D THR* 4.3 0.4 - - - -
242D ASN* 2.6 28.6 + - - +
266D Y0R 3.9 4.7 - - - -
1260D ZN 2.2 36.2 - - - -
1261D GOL 4.0 7.9 - - - -
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Residues in contact with TRP 97 (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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69D SER* 4.0 2.0 - - - -
70D VAL* 3.8 23.1 - - + -
95D LEU* 3.4 36.8 - - + -
96D HIS* 1.3 74.9 - - - +
98D GLY* 1.3 72.3 + - - +
104D GLY* 3.5 12.3 + - - +
115D PRO 3.9 5.8 - - - +
116D ALA* 3.9 12.1 - - + -
224D LEU 6.0 0.2 - - - +
227D LEU* 3.6 39.5 - - + -
228D SER* 3.5 22.4 - - - +
231D LEU* 3.8 21.3 - - + -
239D LEU* 2.8 44.1 + - + -
240D GLN* 3.7 2.6 - - - +
241D LEU* 3.0 16.5 + - - -
242D ASN* 2.9 33.2 + - - +
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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