Contacts of the helix formed by residues 99 - 107 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232C ILE* 4.0 25.1 + - - +
236C MET 5.4 0.8 + - - -
237C GLY* 4.4 14.7 + - - -
685C SAM 5.0 0.4 + - - -
55D GLU* 5.3 0.2 - - - +
97D LYS 3.5 3.0 + - - -
98D GLN* 1.3 76.7 - - - +
100D PRO* 1.3 69.3 - - - +
101D ASP* 3.0 21.0 + - - +
102D ILE* 3.1 34.7 + - - +
103D ASN* 3.1 9.8 + - - +
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Residues in contact with PRO 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C ILE* 4.1 19.1 - - + -
98D GLN 3.3 6.7 - - - +
99D SER* 1.3 86.4 - - - +
101D ASP* 1.3 66.7 + - - +
103D ASN* 3.1 10.1 + - + +
104D GLN* 3.0 31.0 + - - +
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Residues in contact with ASP 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C THR* 2.7 25.3 + - - -
229C ARG* 3.0 41.1 + - - +
230C PHE* 4.4 0.2 - - - -
231C VAL* 2.6 34.0 + - - +
232C ILE* 3.0 25.4 + - + +
685C SAM 3.6 8.1 - - - +
99D SER* 3.0 9.8 + - - +
100D PRO* 1.3 81.5 - - - +
102D ILE* 1.3 56.0 + - - +
104D GLN* 2.9 20.8 - - - +
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Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C THR* 3.8 6.4 - - - +
237C GLY 4.0 10.8 - - - +
685C SAM 3.3 91.3 - - + +
98D GLN* 4.3 7.9 - - + +
99D SER* 3.1 19.2 + - - +
101D ASP* 1.3 77.0 - - - +
103D ASN* 1.3 64.5 + - - +
105D GLY* 2.9 15.4 + - - -
106D VAL* 3.4 15.3 + - + +
117D GLY 4.2 15.9 - - - +
302D ILE* 4.2 7.0 - - + -
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Residues in contact with ASN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ARG* 4.4 6.7 - - - +
57D THR* 6.3 1.0 - - - +
98D GLN* 2.9 27.3 + - - +
99D SER 3.1 7.1 + - - +
100D PRO* 3.5 13.5 - - + +
102D ILE* 1.3 80.6 - - - +
104D GLN* 1.3 62.9 + - - +
106D VAL* 3.0 6.1 + - - +
107D ASP* 3.0 56.0 + - - +
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C THR 3.1 20.2 + - - +
228C GLY 3.9 1.8 - - - -
229C ARG* 3.1 34.6 - - - +
100D PRO* 3.0 16.7 + - - +
101D ASP* 2.9 30.4 - - - +
103D ASN* 1.3 75.7 + - - +
105D GLY* 1.3 60.0 - - - +
107D ASP 4.0 6.4 - - - +
108D ARG* 3.7 21.3 + - - +
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Residues in contact with GLY 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C THR* 3.6 20.8 - - - -
102D ILE 2.9 7.1 + - - -
104D GLN* 1.3 82.2 - - - +
106D VAL* 1.3 59.6 + - - +
108D ARG* 3.0 30.7 + - - -
115D GLY* 3.4 4.0 - - - -
303D GLY* 2.9 25.3 - - - +
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Residues in contact with VAL 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685C SAM 6.0 0.2 - - - +
38D ARG* 3.6 13.9 - - + +
98D GLN* 5.2 5.4 - - - +
102D ILE* 3.4 21.4 + - + +
103D ASN* 3.0 10.4 + - - +
105D GLY* 1.3 78.5 - - - +
107D ASP* 1.3 68.4 + - - +
108D ARG 3.7 0.2 - - - -
114D GLN* 3.0 13.7 - - - +
115D GLY 2.8 28.7 + - - +
116D ALA 3.8 6.5 - - - +
117D GLY* 3.7 29.2 - - - -
268D SER* 4.5 9.0 - - - +
302D ILE* 5.6 0.4 - - + -
303D GLY 5.3 0.7 - - - +
338D TYR* 3.4 21.3 - - - +
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LYS* 6.0 2.2 - - - +
38D ARG* 2.4 40.0 + - - -
103D ASN* 3.0 35.0 + - - +
104D GLN* 4.0 6.1 - - - +
106D VAL* 1.3 77.7 - - - +
108D ARG* 1.3 61.4 + - - +
114D GLN* 2.5 28.1 + - - +
338D TYR* 3.1 8.1 + - - -
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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