Contacts of the strand formed by residues 77 - 88 (chain F) in PDB entry 3P6Y
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 77 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57F ASP* 5.1 1.8 + - - -
63F ARG* 4.4 4.2 + - - +
66F ARG* 3.6 23.0 - - - +
67F MET* 3.7 52.6 - - + +
70F GLU* 3.5 22.3 + - - +
71F PHE* 5.2 0.2 - - - -
75F GLY 3.6 3.2 + - - +
76F MET* 1.3 73.4 - - - +
78F ARG* 1.3 63.3 + - - +
79F THR* 4.1 16.6 - - - +
110F GLU* 3.3 38.7 + - + +
111F LEU 6.0 0.4 - - - +
169F LYS 3.0 13.6 + - - +
170F GLU* 3.4 17.4 + - + +
171F HIS* 2.9 27.4 + - - -
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Residues in contact with ARG 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F MET* 3.6 27.2 + - + +
77F ARG* 1.3 78.6 - - - +
79F THR* 1.3 59.8 + - - +
110F GLU* 3.5 5.7 - - - +
111F LEU* 2.9 64.4 + - + +
112F ASN 3.1 27.5 + - - -
113F PRO* 4.2 2.0 - - - +
114F GLY* 3.4 10.1 - - - +
115F GLU 3.0 32.5 + - - +
117F GLU* 4.7 10.5 + - - +
171F HIS* 3.7 11.9 - - - +
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Residues in contact with THR 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F ARG* 4.2 8.3 - - - -
78F ARG* 1.3 77.8 + - - +
80F VAL* 1.3 75.5 + - - +
81F GLU* 4.3 7.9 - - + +
109F GLY* 3.3 21.3 - - - +
110F GLU* 4.6 2.2 - - + +
111F LEU* 5.4 0.2 - - - +
170F GLU* 2.9 30.0 + - - +
171F HIS 3.1 7.3 + - - +
172F LYS* 3.5 29.0 - - - -
173F LYS* 2.8 24.3 + - - +
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Residues in contact with VAL 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F THR* 1.3 80.6 - - - +
81F GLU* 1.3 71.6 + - - +
108F GLY* 3.3 2.3 - - - -
109F GLY 3.1 24.8 + - - +
111F LEU* 4.0 24.7 - - + -
117F GLU* 3.9 19.3 - - + +
121F LEU* 3.9 24.7 - - + -
124F LEU* 3.7 26.9 - - + -
173F LYS* 3.2 9.6 - - + +
175F PHE* 4.1 18.6 - - + -
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Residues in contact with GLU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F THR* 4.3 9.3 - - + +
80F VAL* 1.3 82.2 - - - +
82F GLY* 1.3 60.6 + - - +
105F LYS* 6.0 1.0 - - - +
106F LEU* 3.4 40.4 + - + +
107F PRO 3.5 7.6 - - - +
108F GLY* 4.5 8.3 - - - -
109F GLY* 5.9 0.2 - - - -
121F LEU* 4.0 6.3 - - - +
172F LYS* 3.4 42.8 + - + +
173F LYS 2.8 9.1 + - - -
174F LEU* 3.3 15.5 - - + +
175F PHE 2.9 26.0 + - - +
211F ILE* 5.3 1.9 - - - +
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Residues in contact with GLY 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F GLU* 1.3 73.6 - - - +
83F VAL* 1.3 62.3 + - - -
84F LEU* 3.8 1.6 + - - -
106F LEU* 3.8 8.4 - - - +
107F PRO* 2.8 37.5 + - - +
121F LEU* 3.8 3.1 - - - +
125F MET* 3.2 26.3 - - - +
175F PHE 3.4 6.1 - - - -
177F VAL* 3.8 5.4 - - - -
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Residues in contact with VAL 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F GLY* 1.3 75.2 - - - +
84F LEU* 1.3 60.6 + - - +
85F ILE* 3.5 25.4 + - + +
94F VAL* 3.9 27.1 - - + -
106F LEU* 4.3 17.3 - - + -
145F ILE* 3.6 28.3 - - + -
174F LEU* 4.6 8.1 - - + -
175F PHE 2.8 15.2 + - - +
176F LEU* 3.9 5.0 - - - +
177F VAL* 3.2 21.0 + - - +
215F LEU* 4.2 17.3 - - + -
219F LEU* 4.4 6.1 - - + -
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Residues in contact with LEU 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F GLY 3.8 1.0 + - - -
83F VAL* 1.3 70.7 - - - +
85F ILE* 1.3 60.0 + - - +
86F VAL 4.1 0.2 - - - -
94F VAL* 3.7 3.1 - - - -
95F LEU* 3.0 62.7 + - + +
107F PRO* 4.0 14.3 - - + +
125F MET* 3.7 31.6 - - + -
129F LEU* 4.1 20.0 - - + -
139F TRP* 4.4 7.4 - - + -
177F VAL* 3.8 21.3 - - + -
179F LEU* 3.8 28.7 - - + -
185F PHE* 4.4 8.7 - - + -
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Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39F LEU* 3.3 37.5 - - + +
40F TYR 5.3 0.5 + - - -
45F TYR* 5.2 1.0 + - - -
83F VAL* 3.5 16.3 + - + +
84F LEU* 1.3 78.2 - - - +
86F VAL* 1.3 77.8 + - - +
92F PRO* 4.1 13.2 - - + -
93F HIS 3.5 7.6 - - - +
94F VAL* 4.7 3.8 - - + -
176F LEU* 3.6 35.7 - - + -
177F VAL 4.1 7.1 + - - +
179F LEU* 4.0 13.5 + - - +
219F LEU* 3.6 26.2 - - + -
224F PHE* 4.0 13.2 - - + -
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Residues in contact with VAL 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 3.7 5.4 - - - +
40F TYR 3.7 11.2 - - - +
42F LEU* 4.1 23.1 - - + -
45F TYR* 3.6 31.4 - - + -
47F PHE* 6.1 0.2 - - + -
84F LEU 4.0 0.4 + - - -
85F ILE* 1.3 86.0 - - - +
87F HIS* 1.3 65.6 + - - +
92F PRO* 3.6 1.0 - - - +
93F HIS* 2.8 46.2 + - + +
95F LEU* 3.9 26.9 - - + -
179F LEU* 3.8 12.6 - - + -
195F ALA* 4.3 2.2 - - + -
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Residues in contact with HIS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 3.5 19.3 - - + -
40F TYR 3.2 30.8 + - - -
41F PRO* 3.4 28.7 - - + +
42F LEU 3.5 2.6 + - - -
86F VAL* 1.3 79.1 - - - +
88F GLU* 1.3 69.6 + - - +
89F HIS* 4.2 5.2 - - - -
90F ARG* 3.2 32.9 + - + -
91F LEU 3.4 14.1 - - - +
93F HIS* 4.1 2.9 - - - +
226F TYR* 3.7 30.9 - + + +
227F ASN 2.8 24.6 + - - -
228F LEU* 4.8 7.6 - - + -
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Residues in contact with GLU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F PRO* 6.0 0.9 - - - -
42F LEU* 3.6 35.1 - - + +
87F HIS* 1.3 80.2 - - - +
89F HIS* 1.3 92.5 + - + +
90F ARG 3.1 2.0 - - - -
91F LEU* 3.0 24.4 + - - +
93F HIS* 3.4 37.5 + - + +
195F ALA* 4.3 3.1 - - - +
90H TRP* 4.9 1.5 - - + -
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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