Contacts of the helix formed by residues 99 - 107 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU* 5.3 0.2 - - - +
97A LYS 3.5 3.4 + - - -
98A GLN* 1.3 81.0 - - - +
100A PRO* 1.3 70.1 - - - +
101A ASP* 3.1 24.8 + - - +
102A ILE* 3.1 23.8 + - - +
103A ASN* 3.2 9.8 + - - +
232B ILE* 4.1 25.3 + - - +
236B MET 5.4 1.3 + - - -
237B GLY* 4.3 17.7 + - - -
484B ANP 5.8 0.2 - - - -
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Residues in contact with PRO 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN 3.3 7.4 - - - +
99A SER* 1.3 86.0 - - - +
101A ASP* 1.3 65.0 + - - +
103A ASN* 3.5 10.5 - - + +
104A GLN* 3.0 30.9 + - - +
232B ILE* 4.4 18.4 - - + -
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A SER* 3.1 10.7 + - - +
100A PRO* 1.3 81.8 - - - +
102A ILE* 1.3 58.1 + - - +
104A GLN* 3.1 12.4 - - - +
227B THR* 2.7 31.0 + - - -
229B ARG* 3.1 42.2 + - - +
230B PHE* 4.6 0.2 - - - -
231B VAL* 2.9 30.0 + - - +
232B ILE* 3.2 25.7 + - + +
484B ANP 3.7 8.1 - - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 4.2 9.0 - - + +
99A SER* 3.1 18.0 + - - +
101A ASP* 1.3 76.6 - - - +
103A ASN* 1.3 60.5 + - - +
105A GLY* 2.9 22.0 + - - -
106A VAL* 3.3 15.3 + - + +
117A GLY* 4.1 18.8 - - - +
302A ILE* 4.3 4.9 - - + +
485A MET* 3.5 58.1 - - + +
227B THR* 4.0 5.4 - - - +
237B GLY 4.2 10.1 - - - +
484B ANP 3.4 32.1 - - + +
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 4.3 7.5 - - - +
57A THR* 6.3 0.6 - - - +
98A GLN* 2.9 28.5 + - - +
99A SER 3.2 6.7 + - - +
100A PRO* 3.2 13.9 + - + +
102A ILE* 1.3 81.5 - - - +
104A GLN* 1.3 61.7 + - - +
106A VAL* 3.0 6.0 + - - +
107A ASP* 3.0 56.1 + - - +
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PRO* 3.0 17.0 + - - +
101A ASP* 3.1 34.7 - - - +
103A ASN* 1.3 74.9 - - - +
105A GLY* 1.3 59.9 + - - +
107A ASP 3.9 6.0 - - - +
108A ARG* 3.6 23.0 + - - +
227B THR 2.8 24.1 + - - +
228B GLY* 4.0 2.0 - - - -
229B ARG* 3.3 25.5 - - - +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE 2.9 9.9 + - - -
104A GLN* 1.3 83.3 - - - +
106A VAL* 1.3 59.1 + - - +
108A ARG* 3.0 29.7 + - - -
115A GLY* 3.5 3.1 - - - -
303A GLY* 2.9 31.9 - - - +
227B THR* 3.8 12.3 - - - -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.5 19.7 - - + +
98A GLN* 5.3 4.9 - - - +
102A ILE* 3.3 20.6 + - + +
103A ASN* 3.0 11.9 + - - +
105A GLY* 1.3 78.1 - - - +
107A ASP* 1.3 62.7 + - - +
108A ARG* 3.5 0.6 + - - -
114A GLN* 3.1 13.0 - - - +
115A GLY 2.8 32.5 + - - +
116A ALA 3.8 4.0 - - - +
117A GLY* 3.7 30.1 - - - -
268A SER* 4.6 8.7 - - - +
269A LYS* 6.3 0.4 - - - +
302A ILE* 5.6 0.7 - - + -
303A GLY 5.4 0.2 - - - +
338A TYR* 3.4 21.5 - - - +
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LYS* 5.8 1.9 - - - +
38A ARG* 2.4 41.0 + - - -
103A ASN* 3.0 34.9 + - - +
104A GLN* 3.9 6.8 - - - +
106A VAL* 1.3 76.8 - - - +
108A ARG* 1.3 62.5 + - - +
114A GLN* 2.4 27.5 + - - +
338A TYR* 3.2 8.3 + - - -
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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