Contacts of the helix formed by residues 97 - 105 (chain E) in PDB entry 1PF7
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 THR 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93E LEU 2.6 20.9 + - - +
94E TRP* 3.9 5.8 - - - -
96E VAL* 1.3 74.9 - - + +
98E PHE* 1.3 64.8 + - - +
99E PRO* 3.3 2.9 - - - -
100E VAL* 3.2 23.0 + - - +
101E ARG* 3.4 7.5 + - - +
146E PRO* 3.7 5.1 + - + +
223E PRO* 3.3 49.1 - - + +
224E GLU* 3.4 7.4 - - - +
227E VAL* 3.4 27.7 - - + +
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Residues in contact with PHE 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E TYR* 3.5 33.9 - + + -
10E TYR* 3.3 48.7 - + - -
13E THR* 3.5 24.9 - - + -
55E ASN* 3.8 9.0 - - + -
56E PHE* 3.6 31.4 - + - -
57E PRO* 3.6 15.5 - - + -
94E TRP 3.8 13.1 + - - +
95E LYS 3.2 11.9 + - - +
97E THR* 1.3 76.0 + - - +
99E PRO* 1.4 79.4 - - + +
101E ARG* 3.0 13.2 + - - +
102E VAL* 3.1 30.9 + - + +
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Residues in contact with PRO 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ILE* 5.8 0.7 - - + -
56E PHE* 3.7 19.1 - - + -
81E MET* 3.5 38.6 - - + -
85E PHE* 3.9 9.0 - - + -
95E LYS 3.6 4.5 - - - +
96E VAL 3.3 20.4 - - - +
97E THR* 4.2 0.7 - - - -
98E PHE* 1.4 93.4 - - + +
100E VAL* 1.3 67.9 + - + +
102E VAL* 2.8 13.7 + - + +
103E PHE* 2.8 34.6 + - + -
224E GLU* 5.8 1.6 - - + -
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Residues in contact with VAL 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ILE* 4.4 11.4 - - + -
97E THR* 3.4 7.4 - - - +
98E PHE 3.1 0.4 - - - -
99E PRO* 1.3 75.9 - - + +
101E ARG* 1.3 63.6 + - - +
103E PHE* 3.1 10.5 + - - +
104E HIS* 3.0 23.0 + - - +
111E LEU* 4.7 5.8 - - + -
224E GLU* 3.9 34.8 - - + +
227E VAL* 3.4 27.4 - - + +
228E ALA* 3.5 28.5 - - + -
231E CYS* 5.0 1.3 - - - -
233E LEU* 4.4 10.7 - - + +
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Residues in contact with ARG 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E GLU* 3.1 41.4 + - - +
10E TYR* 3.4 43.1 + - + +
97E THR* 3.7 13.7 - - - +
98E PHE* 3.0 2.7 + - - +
100E VAL* 1.3 75.8 - - - +
102E VAL* 1.3 58.4 + - - +
104E HIS* 3.2 22.9 - - - +
105E LEU* 3.4 13.9 + - - +
146E PRO 5.1 0.6 + - - -
147E LEU* 3.9 12.2 - - - +
152E ASP* 5.5 3.2 - - - +
155E PHE* 3.7 35.8 - - + +
227E VAL* 4.1 15.7 + - + +
230E HIS* 2.9 35.2 + - - +
231E CYS* 4.2 10.3 - - - -
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E TYR* 4.2 12.3 - - + +
13E THR* 4.3 10.5 - - + -
14E ALA* 4.6 2.5 - - - +
17E LEU* 4.1 24.2 - - + -
56E PHE* 4.6 4.5 - - + -
98E PHE* 3.1 53.2 - - + +
99E PRO* 2.8 6.9 + - + +
101E ARG* 1.3 74.3 - - - +
103E PHE* 1.3 80.6 + - + +
104E HIS 3.0 1.6 - - - -
105E LEU* 3.0 9.8 + - - +
106E LEU* 2.9 25.9 + - + +
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Residues in contact with PHE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ALA* 3.2 27.8 - - + -
29E ILE 5.3 0.4 - - - -
30E ILE* 4.6 17.7 - - + -
56E PHE* 4.8 0.4 - + - -
68E LEU* 3.7 36.3 - - + -
79E VAL* 4.1 17.9 - - + -
81E MET* 4.5 7.6 - - + -
99E PRO* 2.8 39.7 + - + -
100E VAL* 3.5 11.0 - - - +
102E VAL* 1.3 85.8 - - + +
104E HIS* 1.3 64.1 + - - +
106E LEU* 3.0 24.0 + - + +
107E GLY 3.1 0.3 + - - -
108E VAL* 3.0 38.8 + - + +
111E LEU* 4.4 5.4 - - + -
233E LEU* 5.3 2.7 - - + -
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Residues in contact with HIS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E VAL 3.0 7.7 + - - +
101E ARG 3.2 8.7 - - - +
103E PHE* 1.3 76.7 - - - +
105E LEU* 1.3 68.3 + - + +
107E GLY* 3.1 19.8 + - - -
108E VAL* 4.0 10.1 + - - +
154E ARG 4.3 9.1 + - - -
155E PHE* 3.6 37.6 + + - -
231E CYS* 3.5 43.1 + - + -
233E LEU* 4.0 13.3 - - + +
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E TYR* 3.6 25.6 - - + +
10E TYR* 3.5 19.3 - - + +
11E LYS* 3.4 39.3 - - + +
14E ALA* 3.4 20.0 - - + +
15E GLU* 5.3 2.2 - - - +
18E LEU* 4.0 8.8 - - - +
101E ARG 3.4 9.8 + - - +
102E VAL* 3.0 4.9 + - - +
104E HIS* 1.3 90.5 - - + +
106E LEU* 1.3 61.3 + - - +
107E GLY 3.2 0.4 - - - -
155E PHE* 4.0 7.9 - - + -
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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