Contacts of the strand formed by residues 75 - 89 (chain C) in PDB entry 3M4D
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 LYS 75 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLU* 3.6 2.9 - - - +
71C GLU* 3.1 53.9 + - + +
72C GLY 4.0 3.5 - - - +
74C ASN* 1.3 81.9 - - - +
76C SER* 1.3 69.2 + - - +
206C ALA* 3.5 3.6 - - - +
257C GLN* 3.5 30.8 + - - +
258C LEU 3.2 9.9 - - - +
259C HIS* 4.3 18.5 + - + +
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Residues in contact with SER 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 3.1 20.6 - - - +
69C SER* 2.7 22.8 + - - -
70C GLU* 4.2 2.9 - - - +
71C GLU* 4.8 1.1 - - - +
75C LYS* 1.3 79.5 - - - +
77C GLY* 1.3 58.2 + - - +
206C ALA* 3.6 4.4 - - - +
207C ALA* 3.6 27.8 - - - +
210C PHE* 3.4 12.3 - - - -
257C GLN* 3.3 6.6 - - - +
258C LEU 3.0 30.9 + - - +
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Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 3.4 6.8 - - - +
68C TYR* 2.9 46.2 + - - -
69C SER* 2.9 16.6 + - - -
76C SER* 1.3 76.5 + - - +
78C LEU* 1.3 59.2 + - - -
210C PHE* 4.0 2.9 - - - -
255C ASP* 4.0 3.1 - - - -
256C TYR 3.5 5.6 - - - -
257C GLN* 4.0 5.6 - - - -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C TYR* 3.5 48.0 - - + +
66C ARG 3.4 36.8 - - - +
67C VAL* 3.8 8.7 - - + +
68C TYR* 3.5 3.7 - - - -
77C GLY* 1.3 73.0 - - - -
79C ALA* 1.3 65.1 + - - +
80C TRP* 3.8 2.9 - - + -
196C PHE* 3.7 26.5 - - + -
210C PHE* 3.8 22.9 - - + -
254C ASP 3.6 0.5 - - - +
255C ASP* 3.6 2.4 - - - -
256C TYR* 2.7 43.7 + - + +
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C GLN 3.4 5.3 - - - +
65C TYR* 3.3 3.5 - - - -
66C ARG* 2.9 37.4 + - + +
68C TYR* 3.7 13.2 - - + -
78C LEU* 1.3 73.4 - - - +
80C TRP* 1.3 59.9 + - - +
253C ARG* 3.7 23.6 - - - +
254C ASP 3.4 6.1 - - - -
274C TRP* 3.6 23.6 - - + -
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Residues in contact with TRP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLN 4.9 0.4 - - - -
65C TYR* 3.9 20.9 - - + +
78C LEU* 3.8 12.1 - - + -
79C ALA* 1.3 74.7 - - - +
81C PRO* 1.3 99.0 - - + +
82C SER* 3.3 7.4 + - - -
171C PHE* 3.5 32.8 - + - -
184C ARG* 3.7 26.9 - - + -
195C LEU* 3.9 14.4 - - + -
196C PHE* 3.5 22.3 - + - -
220C LEU* 3.6 11.4 - - + -
253C ARG* 3.0 8.2 - - - +
254C ASP* 2.8 61.2 + - + +
256C TYR* 3.8 7.4 - - + +
269C ASN* 3.0 24.1 + - - -
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Residues in contact with PRO 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLY 3.4 19.7 - - - +
65C TYR 4.5 0.9 - - - +
80C TRP* 1.3 96.3 - - + +
82C SER* 1.3 62.9 + - - +
83C ALA 3.3 1.8 - - - +
84C PHE* 3.7 29.8 - - + -
153C PHE* 3.8 9.5 - - - -
220C LEU* 3.3 49.2 - - + +
251C ARG* 4.1 9.6 - - + -
252C VAL 3.5 7.2 - - - +
253C ARG* 4.3 2.7 - - + -
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Residues in contact with SER 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C TRP* 3.3 19.1 + - - -
81C PRO* 1.3 73.7 - - - +
83C ALA* 1.3 64.8 + - - +
153C PHE* 4.6 0.9 - - - -
170C ILE* 3.5 2.4 - - - +
171C PHE* 2.8 27.3 + - - +
184C ARG* 3.8 17.7 + - - -
252C VAL* 2.8 22.3 + - - +
254C ASP* 2.8 39.6 + - - -
272C ASP* 3.8 0.7 + - - -
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO 3.3 1.8 - - - -
82C SER* 1.3 84.5 + - - +
84C PHE* 1.3 66.3 + - - +
85C LYS* 4.4 12.3 + - + -
169C VAL 3.4 7.0 - - - -
170C ILE* 3.8 20.2 - - + -
251C ARG* 3.4 5.4 - - - +
252C VAL* 2.8 50.6 + - + +
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ILE* 3.5 48.5 - - + -
62C ALA 3.8 7.4 - - - -
63C GLY* 4.0 0.4 - - - -
81C PRO* 3.7 24.2 - - + -
83C ALA* 1.3 75.9 - - - +
85C LYS* 1.3 63.3 + - - +
153C PHE* 4.0 21.8 - + - -
168C LYS* 3.3 3.3 - - - +
169C VAL* 2.7 47.6 + - + +
219C LEU* 3.3 31.9 - - + -
224C PHE* 3.8 39.9 - + + -
250C GLU 3.4 3.6 - - - +
251C ARG* 4.6 3.1 - - + -
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Residues in contact with LYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ILE* 4.0 2.7 - - - +
83C ALA* 4.5 9.6 - - + -
84C PHE* 1.3 82.5 - - - +
86C VAL* 1.3 69.7 + - - +
87C GLN* 4.1 23.2 - - - +
158C GLU* 4.2 14.2 + - - +
167C TRP 3.4 7.9 - - - +
168C LYS* 3.9 21.8 - - + +
170C ILE* 5.7 0.2 - - - -
228C PHE* 5.7 0.7 - - - -
248C ILE 4.3 0.9 - - - -
249C TYR* 3.4 1.2 - - - -
250C GLU* 2.8 56.1 + - + +
252C VAL* 4.3 21.3 - - + +
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Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C THR* 3.5 34.1 - - + +
61C ILE* 4.6 1.8 - - + -
85C LYS* 1.3 80.4 - - - +
87C GLN* 1.3 67.1 + - - +
88C LEU* 4.4 6.7 - - + -
166C GLY* 3.2 2.3 - - - -
167C TRP* 2.9 32.1 + - + -
224C PHE* 5.6 0.9 - - + -
226C PRO* 3.7 33.7 - - + -
228C PHE* 3.8 17.6 - - + -
247C VAL* 4.8 0.4 - - + -
248C ILE 3.3 4.7 - - - +
249C TYR* 4.2 23.3 - - + -
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Residues in contact with GLN 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LYS* 4.1 26.6 - - + +
86C VAL* 1.3 84.7 - - - +
88C LEU* 1.3 66.7 + - - +
89C GLN* 4.3 0.7 - - + -
158C GLU* 4.4 9.5 + - - -
164C LYS* 5.9 5.7 + - - -
165C VAL 3.3 11.0 - - - +
166C GLY* 4.3 6.0 - - - -
167C TRP 5.2 0.8 + - - +
247C VAL* 3.3 4.9 - - - +
248C ILE* 2.8 56.4 + - + +
250C GLU* 4.0 19.9 + - + +
277C ARG* 5.7 1.4 + - - -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ILE* 3.9 28.5 - - + -
57C THR* 4.2 18.2 - - + -
86C VAL* 4.4 3.4 - - + -
87C GLN* 1.3 83.2 - - - +
89C GLN* 1.3 61.4 + - - +
98C ILE* 4.2 2.3 - - + +
163C LYS 4.0 0.6 - - - +
164C LYS* 3.3 4.3 - - - +
165C VAL* 2.8 45.5 + - + +
167C TRP* 3.9 15.3 - - + -
230C THR* 3.5 32.5 - - + +
245C ILE* 4.0 23.6 - - + -
246C ASP 3.2 5.2 - - - +
247C VAL* 4.2 11.9 - - + -
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C GLN* 6.2 0.9 - - + -
88C LEU* 1.3 76.3 - - - +
90C LEU* 1.3 70.8 + - - +
91C PRO* 3.9 2.5 - - + +
98C ILE* 5.5 0.2 - - - -
163C LYS* 3.3 11.9 - - + +
164C LYS* 3.9 31.3 + - + +
245C ILE* 3.5 5.5 - - - +
246C ASP* 2.8 49.1 + - + +
248C ILE* 5.0 11.7 - - + +
277C ARG* 5.9 2.4 - - - +
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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