Contacts of the strand formed by residues 90 - 101 (chain F) in PDB entry 4R2G
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 90 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512E NAG 4.4 16.9 + - - -
33F GLN* 6.3 0.7 - - - +
83F ILE* 4.0 15.9 - - + -
84F CYS 4.4 1.6 - - - -
85F GLU* 3.1 39.9 + - + +
89F GLN* 1.3 74.8 - - - +
91F GLU* 1.3 65.4 + - - +
92F GLU* 3.4 9.8 + - + +
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Residues in contact with GLU 91 (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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2F LYS* 5.8 3.5 - - - +
15F THR 5.2 9.4 - - - +
16F CYS* 5.2 7.0 - - + -
17F THR 6.1 0.7 - - - +
28F TRP* 5.3 0.6 - - + -
82F TYR 3.8 0.9 - - - +
83F ILE* 3.1 7.6 - - - +
84F CYS* 2.9 47.1 + - + +
89F GLN* 3.5 26.0 + - - +
90F LYS* 1.3 72.5 - - - +
92F GLU* 1.3 67.6 + - - +
93F VAL* 5.1 7.0 - - + +
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Residues in contact with GLU 92 (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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1F LYS* 3.6 29.2 + - - +
2F LYS* 3.9 7.1 + - - +
81F THR* 4.6 18.0 - - + +
82F TYR 3.6 2.7 - - - +
83F ILE* 4.3 20.7 - - + +
90F LYS* 3.4 10.1 + - + +
91F GLU* 1.3 81.4 - - - +
93F VAL* 1.3 66.7 + - - +
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Residues in contact with VAL 93 (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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1F LYS 5.9 0.2 - - - -
2F LYS* 3.8 18.4 - - + -
4F VAL* 3.6 30.5 - - + -
14F LEU* 4.3 23.3 - - + -
15F THR 4.6 9.0 - - - +
28F TRP* 4.4 20.2 - - + -
81F THR* 3.3 8.5 - - - +
82F TYR* 2.8 36.4 + - - +
91F GLU* 5.1 7.6 - - + +
92F GLU* 1.3 80.4 - - - +
94F GLN* 1.3 67.8 + - - +
95F LEU 4.2 0.4 - - - -
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Residues in contact with GLN 94 (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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1F LYS* 5.1 3.4 + - - -
2F LYS 3.0 16.5 + - - +
3F VAL* 3.4 19.1 - - + +
4F VAL 2.8 27.7 + - - +
80F ASP 3.5 10.4 + - - +
81F THR* 3.9 19.1 + - + +
93F VAL* 1.3 76.5 - - - +
95F LEU* 1.3 60.6 + - - +
96F LEU* 3.9 28.4 + - + +
164F ASN* 5.6 2.1 + - - -
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Residues in contact with LEU 95 (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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4F VAL* 3.3 20.9 - - + +
5F LEU 4.2 13.0 - - - +
6F GLY* 4.4 3.4 - - - +
12F VAL* 4.2 22.7 - - + -
14F LEU* 4.8 11.0 - - + -
71F ILE* 4.5 6.5 - - + -
74F LEU* 4.0 24.0 - - + -
78F ASP 3.9 17.5 - - - +
79F SER* 3.2 7.4 - - - -
80F ASP 2.8 33.4 + - - +
82F TYR* 4.0 18.3 - - + -
93F VAL 4.2 0.6 - - - -
94F GLN* 1.3 71.4 - - - +
96F LEU* 1.3 66.4 + - - +
97F VAL* 3.9 15.7 - - + -
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Residues in contact with LEU 96 (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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3F VAL* 4.2 13.2 - - + -
4F VAL 2.9 11.8 + - - +
5F LEU* 3.2 6.4 - - + -
6F GLY 2.8 25.1 + - - +
79F SER* 4.2 4.7 - - - -
80F ASP 5.6 0.4 - - - +
94F GLN* 4.4 25.1 - - + +
95F LEU* 1.3 80.3 - - - +
97F VAL* 1.3 62.8 + - - +
98F PHE* 3.6 18.5 - - + -
121F PRO* 4.0 18.6 - - + -
122F PRO 5.3 4.5 - - - +
123F GLY 6.2 0.2 - - - -
124F SER* 4.8 6.3 - - - +
163F GLN* 3.5 35.9 - - + +
164F ASN* 3.5 11.2 - - - +
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Residues in contact with VAL 97 (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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6F GLY 3.2 13.0 - - - +
8F LYS* 4.0 14.1 - - + +
74F LEU* 3.9 24.7 - - + -
75F LYS 3.5 33.7 - - - +
76F ILE* 3.6 12.7 - - + +
79F SER* 3.1 22.0 + - - +
95F LEU* 3.9 27.8 - - + -
96F LEU* 1.3 76.3 - - - +
98F PHE* 1.3 60.4 + - - +
121F PRO* 3.1 21.8 - - - +
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Residues in contact with PHE 98 (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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5F LEU* 4.0 23.6 - - + -
6F GLY 2.9 10.4 + - - +
7F LYS* 3.5 1.4 - - - -
8F LYS* 2.9 24.4 + - - -
76F ILE* 4.8 0.7 - - - -
96F LEU* 3.6 31.0 - - + -
97F VAL* 1.3 73.7 - - - +
99F GLY* 1.3 60.2 + - - +
118F LEU* 4.3 9.0 - - + -
119F GLU 3.5 6.7 - - - +
120F SER* 3.3 28.5 - - - -
121F PRO* 3.8 7.9 - - + -
124F SER* 4.0 7.0 - - - -
126F PRO* 3.6 18.4 - - + -
161F VAL* 4.1 14.4 - - + -
163F GLN* 3.6 28.7 - - + -
168F VAL* 4.8 4.3 - - + -
170F PHE* 3.2 23.5 - - + -
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Residues in contact with GLY 99 (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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8F LYS* 4.1 18.6 - - - +
76F ILE* 4.4 1.8 - - - +
98F PHE* 1.3 75.2 - - - +
100F LEU* 1.3 59.8 + - - -
101F THR* 4.0 1.8 - - - -
118F LEU* 3.0 12.5 - - - +
119F GLU* 2.9 42.6 + - - +
170F PHE* 3.8 3.8 - - - -
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Residues in contact with LEU 100 (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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99F GLY* 1.3 74.8 - - - +
101F THR* 1.3 59.8 + - - +
102F ALA 4.3 0.2 + - - -
116F LEU* 4.0 24.0 - - + -
117F THR 3.4 16.8 - - - +
118F LEU* 4.3 6.7 - - + -
128F VAL* 3.7 30.5 - - + -
130F CYS* 5.1 0.4 - - - -
144F LEU* 5.2 2.5 - - + -
159F CYS* 3.9 15.5 - - + -
161F VAL* 3.9 16.2 - - + -
170F PHE* 3.4 32.1 - - + -
172F ILE* 3.9 31.7 - - + +
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Residues in contact with THR 101 (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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8F LYS* 6.3 0.2 - - - +
99F GLY 5.6 1.6 - - - -
100F LEU* 1.3 76.7 - - - +
102F ALA* 1.3 62.7 + - - +
103F ASN* 3.3 19.8 + - + +
116F LEU* 3.7 5.0 - - - +
117F THR* 2.9 44.6 + - + +
119F GLU* 5.2 12.3 - - + +
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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