Contacts of the helix formed by residues 99 - 107 (chain B) in PDB entry 1P7L
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 SER 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ILE* 4.1 24.7 + - - +
236A MET 5.4 1.3 + - - -
237A GLY* 4.4 15.2 + - - -
384A ANP 5.7 0.2 - - - -
55B GLU* 5.3 0.8 - - - +
97B LYS 3.5 3.4 + - - -
98B GLN* 1.3 78.3 - - - +
100B PRO* 1.3 70.7 - - - +
101B ASP* 3.1 21.1 + - - +
102B ILE* 3.1 31.9 + - - +
103B ASN* 3.2 9.4 + - - +
385B MET* 4.9 1.0 + - - -
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ILE* 4.5 17.9 - - + -
98B GLN 3.3 7.2 - - - +
99B SER* 1.3 84.9 - - - +
101B ASP* 1.3 65.8 + - - +
103B ASN* 3.1 10.5 + - + +
104B GLN* 3.0 30.8 + - - +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A THR* 2.8 23.2 + - - -
229A ARG* 3.1 41.1 + - - +
230A PHE* 3.6 0.4 - - - -
231A VAL* 2.8 31.5 + - - +
232A ILE* 3.2 24.6 + - + +
384A ANP 3.7 7.4 - - - +
99B SER* 3.1 10.5 + - - +
100B PRO* 1.3 81.7 - - - +
102B ILE* 1.3 58.4 + - - +
104B GLN* 2.9 21.9 - - - +
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A THR* 3.9 5.6 - - - +
237A GLY 4.1 11.0 - - - +
384A ANP 3.4 32.3 - - + +
98B GLN* 4.3 8.7 - - + +
99B SER* 3.1 18.2 + - - +
101B ASP* 1.3 76.1 - - - +
103B ASN* 1.3 65.3 + - - +
105B GLY* 3.0 14.0 + - - -
106B VAL* 3.4 15.1 + - + +
117B GLY 4.0 19.7 - - - +
302B ILE* 4.2 7.3 - - + +
385B MET* 3.5 55.2 - - + +
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ARG* 4.3 6.7 - - - +
57B THR* 6.4 0.2 - - - +
98B GLN* 2.9 28.2 + - - +
99B SER 3.2 6.7 + - - +
100B PRO* 3.1 14.6 + - + +
102B ILE* 1.3 79.9 - - - +
104B GLN* 1.3 62.7 + - - +
106B VAL* 2.9 16.3 + - - +
107B ASP* 3.0 44.9 + - - +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A THR 2.8 25.3 + - - +
228A GLY* 4.0 2.0 - - - -
229A ARG* 3.3 26.2 - - - +
100B PRO* 3.0 16.1 + - - +
101B ASP* 2.9 32.3 - - - +
103B ASN* 1.3 74.6 - - - +
105B GLY* 1.3 58.7 + - - +
107B ASP 4.0 6.5 - - - +
108B ARG* 3.6 22.7 + - - +
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A THR* 3.9 11.8 - - - -
102B ILE 3.0 9.2 + - - -
104B GLN* 1.3 82.3 - - - +
106B VAL* 1.3 59.4 + - - +
108B ARG* 3.0 30.5 + - - -
115B GLY* 3.4 3.6 - - - -
303B GLY* 2.9 31.4 - - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ARG* 3.5 14.4 - - + +
98B GLN* 5.2 5.4 - - - +
102B ILE* 3.4 21.0 + - + +
103B ASN* 2.9 12.4 + - - +
105B GLY* 1.3 79.1 - - - +
107B ASP* 1.3 67.7 + - - +
108B ARG 3.7 0.2 - - - -
114B GLN* 3.1 12.8 - - - +
115B GLY 2.8 32.1 + - - +
116B ALA 3.8 4.0 - - - +
117B GLY* 3.7 29.4 - - - -
268B SER* 4.5 8.5 - - - +
269B LYS* 6.3 0.2 - - - +
302B ILE* 5.6 0.7 - - + -
303B GLY 5.3 0.4 - - - +
338B TYR* 3.4 20.4 - - - +
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 6.0 1.8 - - - +
38B ARG* 2.4 39.7 + - - -
103B ASN* 3.0 34.4 + - - +
104B GLN* 4.0 6.8 - - - +
106B VAL* 1.3 76.6 - - - +
108B ARG* 1.3 63.1 + - - +
114B GLN* 2.5 28.0 + - - +
338B TYR* 3.1 9.5 + - - -
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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