Contacts of the strand formed by residues 92 - 100 (chain H) in PDB entry 3PP4
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 ALA 92 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38H ARG* 4.2 9.6 - - - -
39H GLN 3.4 18.8 - - - +
40H ALA* 3.7 13.0 - - + +
41H PRO* 4.5 3.1 - - - -
90H ASP 3.1 11.0 + - - +
91H THR* 1.3 78.5 - - - +
93H VAL* 1.3 63.4 + - - +
94H TYR* 3.4 19.5 - - + -
114H LEU* 3.9 5.2 - - - -
115H VAL 2.9 31.1 + - - -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 3.3 1.9 - - - -
39H GLN* 2.8 47.6 + - + +
92H ALA* 1.3 73.5 - - - +
94H TYR* 1.3 62.9 + - - +
95H TYR* 3.6 36.4 + - + +
111H GLN 5.0 0.9 - - - +
112H GLY* 3.8 18.8 - - - -
113H THR 3.4 7.6 - - - +
114H LEU* 4.0 22.7 - - + +
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Residues in contact with TYR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLN* 2.8 28.6 + - - -
18H VAL* 6.0 1.3 - - + -
20H VAL* 4.6 13.9 - - + -
36H TRP* 4.7 9.2 - + + -
37H VAL 3.8 2.0 - - - -
38H ARG* 3.0 32.5 + - + -
48H MET* 3.4 41.3 - - + -
81H MET* 3.6 18.2 - - + -
83H LEU* 3.4 13.0 - - + +
86H LEU* 5.1 0.6 - - + +
90H ASP* 2.6 30.4 + - - +
92H ALA* 3.4 20.9 - - + -
93H VAL* 1.3 72.7 - - - +
95H TYR* 1.3 55.7 + - - +
112H GLY* 3.3 0.2 - - - -
113H THR 2.8 24.7 + - - +
115H VAL* 3.8 26.0 - - + -
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Residues in contact with TYR 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLN* 3.5 1.8 - - - -
36H TRP* 3.3 10.0 - - - -
37H VAL* 2.7 45.4 + - - +
39H GLN* 3.6 23.5 + - + -
45H LEU* 4.8 4.0 - - + -
93H VAL* 3.6 28.3 - - + +
94H TYR* 1.3 74.3 - - - +
96H CYS* 1.3 61.3 + - - +
109H TRP* 3.7 28.7 - + + -
110H GLY 3.6 13.7 - - - -
111H GLN 3.8 3.6 + - - -
112H GLY* 3.5 21.3 - - - -
43L GLN* 2.7 28.7 + - - -
47L GLN 4.3 1.7 + - - -
48L SER* 3.6 18.8 - - - -
49L PRO* 3.9 14.4 - - + -
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Residues in contact with CYS 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.0 11.9 - - - -
6H GLN* 3.0 26.2 + - - -
22H CYS* 2.0 53.8 - - + -
34H ILE* 4.1 3.8 - - + -
35H ASN 3.2 8.5 - - - +
36H TRP* 3.8 15.9 - - + -
95H TYR* 1.3 78.6 - - - +
97H ALA* 1.3 64.4 + - - +
109H TRP* 3.5 1.0 - - - -
110H GLY* 2.9 24.8 + - - -
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Residues in contact with ALA 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.1 3.4 - - - -
34H ILE* 3.5 4.1 - - - +
35H ASN* 2.7 41.8 + - + +
37H VAL* 5.4 1.8 - - + -
96H CYS* 1.3 78.1 - - - +
98H ARG* 1.3 60.3 + - - +
99H ASN 3.8 0.2 + - - -
106H LEU* 4.1 21.1 - - + -
108H TYR 3.1 11.9 - - - +
109H TRP* 3.8 30.1 - - + -
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Residues in contact with ARG 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H VAL* 3.7 8.2 - - - +
4H LEU* 3.7 12.4 - - + +
27H TYR* 3.6 51.3 - - + +
32H SER* 3.0 32.2 + - - -
33H TRP 3.6 5.2 - - - +
34H ILE* 4.1 11.4 - - + -
97H ALA* 1.3 70.8 - - - +
99H ASN* 1.3 71.0 + - - +
100H VAL* 3.6 24.0 + - - +
101H PHE 5.5 0.8 - - - +
105H TRP 3.5 9.2 - - - +
106H LEU* 3.6 4.2 - - - -
107H VAL 3.5 13.2 + - - -
108H TYR* 2.8 44.3 + - + +
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Residues in contact with ASN 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H SER* 3.6 15.6 + - - -
33H TRP* 3.0 22.9 + - + +
35H ASN* 4.0 3.1 - - - +
97H ALA 3.8 2.0 + - - -
98H ARG* 1.3 81.9 - - - +
100H VAL* 1.3 63.2 + - - +
101H PHE* 3.6 21.0 + - - -
105H TRP* 3.1 35.3 - - - -
106H LEU* 3.9 5.5 - - + +
225H CL 3.5 25.3 - - + +
173P SER* 2.8 30.8 + - - +
174P GLU* 5.3 0.3 - - - +
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Residues in contact with VAL 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H ARG* 4.0 20.9 - - - +
99H ASN* 1.3 77.7 - - - +
101H PHE* 1.3 76.0 + - - +
103H GLY 4.1 0.5 + - - -
104H TYR* 3.4 24.7 + - + -
105H TRP 2.8 33.2 + - - +
107H VAL* 3.8 13.2 - - + -
108H TYR* 3.6 37.9 - - + -
174P GLU* 4.6 0.5 - - - +
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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