Contacts of the strand formed by residues 69 - 84 (chain D) in PDB entry 4IYC
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 ILE 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D TYR* 3.1 49.5 + - + -
66D THR* 3.2 23.7 + - + +
68D HIS* 1.3 109.7 - - + +
70D LYS* 1.3 66.2 + - - +
238D HIS* 4.3 18.8 - - + -
239D ALA 3.5 5.4 - - - +
240D THR* 3.7 24.9 - - + +
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Residues in contact with LYS 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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61D TYR 3.5 9.2 - - - +
62D ASN* 3.1 29.9 + - - +
63D TYR* 4.0 3.8 - - - +
66D THR 4.5 0.6 + - - -
67D ASP* 3.2 32.2 + - - +
69D ILE* 1.3 77.5 - - - +
71D ALA* 1.4 56.9 + - - +
185D SER 3.4 22.4 - - - -
186D GLN* 3.6 16.1 + - - +
187D ASN 4.0 0.7 - - - +
188D PRO* 3.7 23.8 - - + +
191D TYR* 3.5 37.9 - - + -
192D PHE* 3.8 3.8 - - - -
238D HIS* 3.6 2.0 - - - -
239D ALA* 2.7 35.3 + - - +
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Residues in contact with ALA 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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60D TYR* 3.2 4.9 - - - +
61D TYR* 2.7 65.0 + - + -
63D TYR* 4.8 2.0 - - + +
70D LYS* 1.4 73.3 - - - +
72D MET* 1.3 59.7 + - - +
73D ARG 4.3 0.7 - - - -
188D PRO* 4.6 0.2 - - - +
192D PHE* 3.5 8.7 - - - -
236D VAL* 4.1 3.1 - - + -
237D THR 3.3 12.8 - - - +
238D HIS* 3.6 23.3 - - + -
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Residues in contact with MET 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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58D THR* 4.1 3.4 - - + -
59D THR 3.2 6.5 - - - +
60D TYR* 3.5 36.8 - - + +
71D ALA* 1.3 74.4 - - - +
73D ARG* 1.3 59.0 + - - +
74D TRP* 3.5 19.5 - - + -
178D PHE* 3.7 40.2 - - + -
192D PHE* 3.7 26.9 - - + -
198D LEU* 4.1 6.1 - - + -
202D VAL* 3.6 31.6 - - + -
236D VAL* 3.4 2.3 - - - -
237D THR* 2.9 32.3 + - - -
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Residues in contact with ARG 73 (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 LYS 4.1 6.8 + - - +
58D THR* 3.4 7.8 - - - +
59D THR* 2.8 62.2 + - - +
61D TYR* 4.0 25.2 + - + -
71D ALA 4.3 0.4 - - - -
72D MET* 1.3 69.5 - - - +
74D TRP* 1.3 61.8 + - - +
234D MET* 3.9 21.7 - - + +
235D ASP 3.2 10.8 - - - +
236D VAL* 4.2 10.8 - - + +
260D PHE* 3.6 37.9 - - - -
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Residues in contact with TRP 74 (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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58D THR* 4.3 1.8 - - - +
72D MET* 3.5 46.9 - - + -
73D ARG* 1.3 74.6 - - - +
75D PRO* 1.4 95.5 - - + +
76D PHE* 3.3 22.8 + + - -
142D TYR* 3.9 10.5 - - - -
160D ALA* 4.1 8.5 - - + -
172D GLY 4.2 0.9 - - - -
177D LEU* 3.9 11.2 - - + -
178D PHE* 3.5 33.2 - + - -
202D VAL* 4.2 5.8 - - + -
234D MET* 3.4 8.4 - - - -
235D ASP* 2.8 47.9 + - + +
237D THR* 3.2 19.7 + - - +
255D ARG* 3.4 37.2 - - - -
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Residues in contact with PRO 75 (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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56D SER* 3.4 23.3 - - - +
58D THR* 3.5 11.7 - - - +
74D TRP* 1.4 85.6 - - + +
76D PHE* 1.3 60.2 + - - +
77D GLN 4.6 0.7 - - - +
78D TYR* 3.4 36.1 - - + +
142D TYR* 2.7 29.8 + - - -
201D LEU 3.4 11.0 - - - +
202D VAL* 4.6 4.0 - - - -
232D ARG* 4.4 7.4 - - + -
233D ASN 3.6 1.1 - - - +
234D MET* 3.0 20.4 - - + -
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Residues in contact with PHE 76 (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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74D TRP* 3.3 15.2 + + - -
75D PRO* 1.3 73.4 - - - +
77D GLN* 1.3 68.2 + - + +
142D TYR* 3.6 2.6 - - - -
159D LYS* 3.4 20.6 - - + -
160D ALA* 2.8 52.5 + - + +
172D GLY 3.2 30.7 - - - -
173D HIS* 3.6 21.3 - + - -
233D ASN 2.9 10.7 + - - +
235D ASP* 3.3 29.4 - - + +
257D HIS* 3.5 34.5 - + - -
258D ASN* 4.6 6.5 - - - +
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Residues in contact with GLN 77 (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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75D PRO 3.3 1.5 - - - -
76D PHE* 1.3 91.1 - - + +
78D TYR* 1.3 71.2 + - - +
79D ASN* 3.2 25.1 + - - +
147D GLU* 4.5 11.9 + - - +
157D GLY* 4.0 15.7 - - - -
158D ILE 3.3 11.7 - - - +
159D LYS* 3.3 28.8 - - - +
232D ARG* 3.2 5.0 - - - +
233D ASN* 2.8 53.1 + - + +
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Residues in contact with TYR 78 (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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54D ILE* 3.6 39.7 - - + -
55D ASN 4.4 3.8 - - - -
56D SER* 3.4 3.3 - - - -
75D PRO* 3.4 25.1 - - + +
77D GLN* 1.3 75.1 - - - +
79D ASN* 1.3 61.5 + - - +
142D TYR* 4.5 5.8 - + - -
156D TRP 3.8 0.7 - - - +
157D GLY* 3.5 6.4 - - - -
158D ILE* 2.9 44.1 + - + +
201D LEU* 2.5 59.8 + - + -
205D GLY* 3.4 13.0 - - - -
206D PHE* 3.5 40.2 - - + -
231D GLY 3.4 4.3 - - - +
232D ARG* 4.2 4.3 - - + -
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Residues in contact with ASN 79 (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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77D GLN* 3.2 36.6 - - - +
78D TYR* 1.3 72.8 + - - +
80D ILE* 1.3 64.0 + - - +
155D GLN* 4.9 12.1 - - - +
156D TRP 3.6 6.1 + - - +
229D THR* 3.3 3.0 - - + +
230D TYR* 3.3 6.2 - - - -
231D GLY 2.8 36.9 + - - +
232D ARG* 3.8 4.7 - - - -
233D ASN* 3.0 25.5 + - - +
262D ASN* 3.9 9.1 - - - +
264D ASN* 3.2 27.4 - - - +
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Residues in contact with ILE 80 (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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50D MET* 4.8 8.5 - - + -
54D ILE* 3.5 25.8 - - + -
79D ASN* 1.3 83.1 - - - +
81D GLY* 1.3 60.6 + - - +
155D GLN* 3.5 5.5 + - - -
156D TRP* 2.7 63.7 + - + +
158D ILE* 4.9 4.0 - - + -
206D PHE* 4.3 6.3 - - + -
208D PRO* 3.8 17.3 - - + -
210D PHE* 3.7 36.3 - - + -
229D THR 3.3 2.5 - - - -
230D TYR* 4.0 25.1 - - + -
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Residues in contact with GLY 81 (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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50D MET* 5.1 1.1 - - - +
80D ILE* 1.3 78.9 - - - +
82D LEU* 1.3 61.1 + - - +
154D VAL 3.4 9.9 - - - -
155D GLN* 4.1 14.3 - - - +
156D TRP* 5.2 0.9 - - - -
227D GLU 4.4 0.9 - - - -
228D ILE* 3.3 8.7 - - - +
229D THR* 2.8 41.1 + - - -
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Residues in contact with LEU 82 (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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48D LEU* 4.0 23.3 - - + -
50D MET* 4.2 16.2 - - - -
81D GLY* 1.3 74.1 - - - +
83D LYS* 1.3 66.4 + - - +
91D LEU* 3.8 29.2 - - + -
152D LYS 5.5 2.7 - - - +
153D SER* 3.2 5.8 - - - -
154D VAL* 3.0 41.0 + - + +
156D TRP* 5.5 0.4 - - - -
212D ALA* 3.8 13.9 - - + -
214D VAL* 4.5 11.0 - - + -
226D PHE* 4.3 15.5 - - + -
227D GLU 3.4 5.4 - - - +
228D ILE* 3.7 23.8 - - + -
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Residues in contact with LYS 83 (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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82D LEU* 1.3 80.0 - - - +
84D THR* 1.3 66.1 + - - +
152D LYS 3.3 6.3 - - - +
153D SER* 3.6 15.9 - - - -
226D PHE* 3.4 7.3 - - - +
227D GLU* 3.0 68.9 + - + +
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Residues in contact with THR 84 (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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82D LEU* 6.5 0.2 - - - -
83D LYS* 1.3 79.5 - - - +
85D ASN* 1.3 60.6 + - - +
86D ASP* 3.6 16.1 + - - +
89D VAL* 3.7 25.0 - - + +
151D SER 5.0 0.9 - - - +
152D LYS* 3.0 51.7 + - + +
214D VAL* 5.7 2.5 - - + -
224D SER* 5.0 0.2 - - - -
225D GLU 2.9 20.8 + - - -
226D PHE* 3.7 19.2 - - + -
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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