Contacts of the strand formed by residues 75 - 89 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G GLU* 3.9 0.2 - - - -
71G GLU* 3.0 58.6 + - + +
72G GLY 3.1 9.5 + - - +
73G ALA 3.6 1.0 - - - -
74G ASN* 1.3 90.6 - - + +
76G SER* 1.3 65.1 + - - +
206G ALA* 3.6 2.2 - - - +
257G GLN* 5.4 1.6 - - - +
258G LEU 3.3 6.5 - - - +
259G HIS* 3.9 19.1 - - + -
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Residues in contact with SER 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G VAL* 3.2 11.3 - - - +
69G SER* 2.7 23.9 + - - -
70G GLU* 4.5 0.9 - - - -
71G GLU* 4.6 0.9 + - - +
75G LYS* 1.3 77.5 - - - +
77G GLY* 1.3 58.3 + - - +
206G ALA* 3.6 6.9 - - - +
207G ALA* 3.2 40.6 - - - +
210G PHE* 3.3 8.8 - - - -
257G GLN* 3.2 9.6 + - - +
258G LEU 3.0 30.1 + - - -
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Residues in contact with GLY 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G VAL* 3.3 5.9 - - - +
68G TYR* 3.2 28.1 + - - -
69G SER* 2.7 23.5 + - - +
76G SER* 1.3 75.7 + - - +
78G LEU* 1.3 59.6 + - - -
210G PHE* 3.9 3.4 - - - -
256G TYR 3.6 6.3 - - - -
257G GLN* 3.7 20.6 - - - -
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Residues in contact with LEU 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G TYR* 3.4 45.1 - - + +
66G ARG* 3.3 38.4 - - - +
67G VAL* 3.7 9.0 - - + +
68G TYR* 4.0 3.5 - - - -
77G GLY* 1.3 74.3 - - - -
79G ALA* 1.3 65.0 + - - +
80G TRP* 3.8 2.9 - - + -
196G PHE* 3.5 31.6 - - + -
210G PHE* 3.7 17.5 - - + -
254G ASP 3.7 0.3 - - - +
255G ASP* 3.7 2.1 + - - -
256G TYR* 2.9 46.1 + - + +
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Residues in contact with ALA 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLN 3.6 2.6 - - - +
65G TYR* 3.3 3.8 - - - -
66G ARG* 2.8 42.3 + - + +
68G TYR* 3.6 16.1 - - + -
78G LEU* 1.3 72.8 - - - +
80G TRP* 1.3 58.4 + - - +
253G ARG* 3.7 21.5 - - - +
254G ASP 3.4 7.0 - - - -
274G TRP* 3.6 23.8 - - + -
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Residues in contact with TRP 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLN 5.1 0.4 - - - -
65G TYR* 4.0 19.3 - - + -
78G LEU* 3.8 13.5 - - + -
79G ALA* 1.3 74.4 - - - +
81G PRO* 1.3 94.7 - - + +
82G SER* 3.3 7.1 + - - -
171G PHE* 3.4 34.1 - + - -
184G ARG* 3.7 25.6 - - + -
195G LEU* 3.8 15.3 - - + -
196G PHE* 3.5 22.9 - + + -
220G LEU* 3.7 12.6 - - + -
253G ARG* 3.1 8.7 - - - +
254G ASP* 2.8 66.8 + - + +
256G TYR* 3.8 7.3 - - + +
269G ASN* 3.0 26.6 + - - -
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Residues in contact with PRO 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G GLY 3.4 19.7 - - - +
65G TYR 4.3 0.9 - - - +
80G TRP* 1.3 96.7 - - + +
82G SER* 1.3 63.3 + - - +
83G ALA 3.3 1.6 - - - +
84G PHE* 3.7 28.9 - - + -
153G PHE* 3.8 9.0 - - - -
220G LEU* 3.3 48.5 - - + +
251G ARG* 4.1 9.4 - - + -
252G VAL 3.5 7.4 - - - +
253G ARG* 4.1 2.9 - - + -
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Residues in contact with SER 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G TRP* 3.3 19.0 + - - -
81G PRO* 1.3 73.5 - - - +
83G ALA* 1.3 60.8 + - - +
153G PHE* 4.7 0.7 - - - -
170G ILE* 3.5 2.3 - - - +
171G PHE* 2.8 27.7 + - - +
184G ARG* 3.6 19.1 + - - -
252G VAL* 2.9 19.3 + - - +
254G ASP* 2.8 38.0 + - - -
272G ASP* 3.7 6.8 + - - -
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Residues in contact with ALA 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G PRO* 3.3 2.0 + - - +
82G SER* 1.3 85.1 - - - +
84G PHE* 1.3 65.8 + - - +
85G LYS* 4.3 12.3 - - - -
169G VAL 3.4 10.1 - - - +
170G ILE* 4.0 15.9 - - + -
251G ARG* 3.5 5.5 - - - +
252G VAL* 2.8 51.2 + - + +
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Residues in contact with PHE 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ILE* 3.7 44.0 - - + -
62G ALA 3.9 11.7 - - - -
81G PRO* 3.7 23.1 - - + -
83G ALA* 1.3 76.7 - - - +
85G LYS* 1.3 62.3 + - - +
86G VAL* 5.9 0.4 - - + -
153G PHE* 3.8 24.2 - + - -
168G LYS* 3.2 3.5 - - - -
169G VAL* 2.8 47.0 + - + +
219G LEU* 3.2 31.0 - - + -
224G PHE* 3.8 40.4 - + + -
250G GLU 3.5 4.0 - - - +
251G ARG* 4.6 3.4 - - + -
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Residues in contact with LYS 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ILE* 4.0 2.3 - - - +
83G ALA* 4.3 10.8 - - + -
84G PHE* 1.3 82.6 - - - +
86G VAL* 1.3 68.8 + - - +
87G GLN* 4.1 20.8 - - + +
158G GLU* 4.2 10.7 + - - +
167G TRP 3.3 8.5 - - - +
168G LYS* 3.8 23.5 - - + +
170G ILE* 5.7 0.2 - - - -
228G PHE* 6.1 0.7 - - - -
248G ILE 4.2 0.9 - - - -
249G TYR* 3.4 1.6 - - - -
250G GLU* 2.8 69.1 + - + +
252G VAL* 4.2 19.0 - - + +
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Residues in contact with VAL 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G THR* 3.6 34.3 - - + +
61G ILE* 4.7 1.8 - - + -
85G LYS* 1.3 80.0 - - - +
87G GLN* 1.3 65.9 + - - +
88G LEU* 4.4 7.2 - - + -
166G GLY* 3.1 3.5 - - - -
167G TRP* 2.9 32.7 + - + -
224G PHE* 5.5 1.1 - - + -
226G PRO* 3.8 30.5 - - + -
228G PHE* 3.8 21.3 - - + -
247G VAL* 4.9 0.7 - - + -
248G ILE 3.3 4.5 - - - +
249G TYR* 3.9 22.0 - - + -
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Residues in contact with GLN 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G LYS* 4.1 25.8 - - + +
86G VAL* 1.3 86.2 - - - +
88G LEU* 1.3 66.1 + - - +
89G GLN* 6.3 0.2 - - + -
158G GLU* 4.2 10.9 + - - -
164G LYS* 6.4 3.1 - - - -
165G VAL 3.4 9.0 - - - +
166G GLY* 4.4 6.5 - - - -
167G TRP 5.0 0.9 - - - +
247G VAL* 3.3 5.2 - - - +
248G ILE* 2.8 60.3 + - + +
250G GLU* 4.7 9.1 + - - +
277G ARG* 5.5 3.3 + - - -
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Residues in contact with LEU 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G ILE* 4.0 28.9 - - + -
57G THR* 4.2 18.6 - - + -
86G VAL* 4.4 3.1 - - + -
87G GLN* 1.3 83.5 - - - +
89G GLN* 1.3 61.9 + - - +
98G ILE* 4.4 2.8 - - + +
163G LYS 4.6 0.2 - - - -
164G LYS* 3.3 4.2 - - - +
165G VAL* 2.8 42.2 + - + +
167G TRP* 3.8 20.0 - - + -
230G THR* 3.6 30.1 - - + +
245G ILE* 4.1 24.0 - - + -
246G ASP 3.3 4.7 - - - +
247G VAL* 4.2 11.2 - - + -
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Residues in contact with GLN 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G GLN* 6.3 0.7 - - + -
88G LEU* 1.3 76.9 - - - +
90G LEU* 1.3 71.9 + - - +
91G PRO* 3.9 2.9 - - + +
163G LYS* 3.3 9.0 - - + +
164G LYS* 4.0 31.0 + - + +
245G ILE* 3.6 7.7 - - - +
246G ASP* 2.9 46.5 + - + +
248G ILE* 5.1 10.2 - - + +
277G ARG* 6.1 1.0 - - - +
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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