Contacts of the strand formed by residues 58 - 72 (chain D) in PDB entry 5FJV
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 58 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 3.9 22.4 - - + -
52D PRO* 4.0 9.6 - - + -
53D ASN* 3.7 22.0 - - + +
57D VAL* 1.3 71.4 - - - +
59D ILE* 1.3 70.8 + - - +
60D VAL* 4.4 2.2 - - + -
89D TRP* 4.3 17.0 - - + -
90D SER 4.6 10.1 - - - +
115D TRP* 4.1 20.9 - - + -
184D LYS 2.8 13.4 + - - +
185D ILE* 3.1 11.5 - - + +
186D ASP 2.9 25.5 + - - -
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Residues in contact with ILE 59 (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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57D VAL* 3.4 24.3 + - + +
58D VAL* 1.3 78.4 - - - +
60D VAL* 1.3 69.3 + - - +
61D ARG* 4.1 3.7 + - + +
88D GLU 3.8 0.3 - - - +
89D TRP* 3.4 21.0 - - - +
90D SER 4.4 1.9 + - - -
186D ASP* 3.2 14.4 - - + +
188D GLU* 4.5 23.3 - - + +
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D VAL* 4.4 4.3 - - + +
59D ILE* 1.3 78.8 - - - +
61D ARG* 1.3 64.9 + - - +
62D PHE* 3.5 1.7 + - + +
87D GLN* 4.5 9.2 - - + -
88D GLU 3.2 23.8 - - - +
89D TRP* 4.1 17.7 - - + -
117D PRO* 4.2 13.7 - - + -
119D ILE* 4.8 6.7 - - + -
185D ILE* 3.2 38.6 - - + -
186D ASP 3.0 7.5 + - - +
187D LEU* 3.4 15.2 - - + +
188D GLU 3.2 21.8 + - - +
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Residues in contact with ARG 61 (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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59D ILE* 4.1 4.0 - - + -
60D VAL* 1.3 70.0 - - - +
62D PHE* 1.3 58.6 + - - +
86D LYS 3.4 1.2 - - - +
87D GLN* 3.3 6.1 - - - -
88D GLU* 2.5 80.9 + - + +
188D GLU* 2.9 39.9 + - + +
189D GLN 4.6 0.8 + - - -
190D MET* 3.5 55.2 - - + +
191D GLU 4.8 1.6 - - - +
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Residues in contact with PHE 62 (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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60D VAL* 4.2 3.1 - - + +
61D ARG* 1.3 76.4 - - - +
63D GLY* 1.3 73.7 + - - +
64D LEU* 5.2 0.4 - - + -
85D LEU* 3.5 29.8 - - + -
86D LYS 3.2 11.0 - - - -
87D GLN* 4.5 7.4 - - + -
119D ILE* 4.6 12.1 - - + -
175D PHE* 3.4 43.3 - + + -
187D LEU* 3.9 33.7 - - + -
188D GLU 3.1 8.8 + - - +
189D GLN* 3.5 7.1 - - - -
190D MET* 2.8 26.8 + - - +
229D VAL* 4.0 15.7 - - + -
231D TYR* 3.6 27.1 + + - -
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Residues in contact with GLY 63 (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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62D PHE* 1.3 82.2 - - - +
64D LEU* 1.3 60.1 + - - -
85D LEU* 3.6 1.4 - - - -
86D LYS* 2.6 66.6 + - - +
190D MET* 4.0 6.7 - - - -
231D TYR* 3.6 6.7 - - - -
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Residues in contact with LEU 64 (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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62D PHE* 5.2 2.0 - - + -
63D GLY* 1.3 72.4 - - - -
65D SER* 1.3 81.1 + - - +
66D ILE* 4.2 6.3 - - + +
83D VAL* 3.9 21.5 - - + -
84D TRP 3.8 2.7 - - - +
85D LEU* 5.0 4.5 - - + +
86D LYS* 4.1 3.3 + - - -
173D MET* 4.2 7.0 - - - -
175D PHE* 3.9 21.8 - - + -
196D LEU* 2.9 31.3 - - + +
231D TYR* 3.5 58.5 + - + -
233D PHE* 4.2 15.3 - - + -
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Residues in contact with SER 65 (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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221C CYS* 4.7 0.5 - - - +
64D LEU* 1.3 81.5 + - - +
66D ILE* 1.3 61.2 + - - +
67D ALA 4.1 0.2 - - - -
83D VAL* 3.3 1.7 - - - +
84D TRP* 2.9 54.1 + - - -
86D LYS* 3.2 24.8 + - - +
196D LEU* 3.6 4.7 - - - +
199D TYR* 3.0 35.2 + - - -
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Residues in contact with ILE 66 (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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64D LEU* 4.6 6.3 - - + -
65D SER* 1.3 75.1 - - - +
67D ALA* 1.3 62.4 + - - +
68D GLN* 3.8 17.9 - - - +
81D THR* 3.8 31.2 - - + -
82D ASN 4.3 3.8 - - - +
83D VAL* 4.6 3.6 - - + +
196D LEU* 2.9 20.6 + - + +
197D LYS* 3.1 39.5 - - + -
199D TYR* 3.4 15.7 - - - -
200D TRP* 3.6 14.9 + - + -
207D ILE* 3.9 21.1 - - + -
233D PHE* 4.2 14.4 - - + -
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Residues in contact with ALA 67 (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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122C TYR 5.0 6.5 - - - +
123C ASN 5.7 0.2 - - - +
65D SER 4.0 1.6 + - - -
66D ILE* 1.3 74.1 - - - +
68D GLN* 1.3 64.7 + - + +
82D ASN* 3.2 29.4 + - - +
83D VAL* 4.6 0.2 - - - +
84D TRP* 3.7 28.4 - - + +
199D TYR* 3.3 23.4 - - + +
200D TRP* 3.9 2.0 - - - -
201D GLU* 3.5 17.2 + - - +
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Residues in contact with GLN 68 (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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77C GLN* 5.3 2.6 + - - -
123C ASN* 3.1 26.2 + - - +
124C ASN* 3.8 19.1 + - - +
156C SER* 2.9 33.9 + - - -
66D ILE* 3.6 5.9 - - - +
67D ALA* 1.3 84.9 - - + +
69D LEU* 1.3 71.9 + - - +
70D ILE* 3.6 13.4 + - + +
81D THR* 3.5 6.4 - - - +
82D ASN* 3.0 38.6 + - + +
200D TRP* 3.2 11.2 - - + -
201D GLU* 4.4 14.9 + - + +
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Residues in contact with LEU 69 (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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77C GLN* 5.1 2.3 + - - -
68D GLN* 1.3 75.8 - - - +
70D ILE* 1.3 67.4 + - - +
71D ASP 4.8 8.7 - - - +
72D VAL* 5.2 2.2 - - + -
79D MET* 3.6 36.3 - - + -
80D THR 3.9 2.7 - - - +
81D THR* 3.8 11.7 - - + -
200D TRP* 2.7 31.4 - - + -
203D GLY* 5.0 9.3 + - - +
204D GLU* 5.1 1.2 - - - +
205D TRP* 3.9 30.7 - - + +
207D ILE* 3.9 30.3 - - + -
235D ILE* 4.1 13.0 - - + -
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Residues in contact with ILE 70 (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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76C ASN* 4.5 2.8 - - - +
77C GLN* 3.7 20.3 + - - -
78C MET* 4.3 17.9 - - + -
124C ASN* 3.6 25.8 - - - +
126C ASP* 4.1 16.6 - - - +
68D GLN* 4.2 23.6 - - - +
69D LEU* 1.3 78.1 - - - +
71D ASP* 1.3 67.9 + - + +
80D THR* 2.8 37.0 + - + +
82D ASN* 4.1 12.8 - - + +
152D ILE* 3.9 18.6 - - + -
204D GLU* 4.8 2.1 - - - +
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Residues in contact with ASP 71 (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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75C LYS* 5.0 9.6 + - - -
76C ASN* 3.0 29.8 + - - +
69D LEU* 3.5 5.3 - - - +
70D ILE* 1.3 90.5 - - + +
72D VAL* 1.3 78.9 + - - +
73D ASP* 4.1 11.5 - - - +
78D MET 4.1 0.2 - - - +
79D MET* 3.4 1.9 - - - +
80D THR* 2.6 39.9 + - - +
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Residues in contact with VAL 72 (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 LEU* 5.2 4.3 - - + -
71D ASP* 1.3 85.6 + - - +
73D ASP* 1.3 62.1 + - - +
74D GLU* 3.3 13.9 - - - +
78D MET 3.3 11.0 - - - +
79D MET* 4.0 8.3 - - + +
160D ASP* 4.4 17.5 - - - +
171D CYS* 4.7 2.7 - - - -
205D TRP* 3.2 60.5 + - + +
235D ILE* 4.1 22.2 - - + -
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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