Contacts of the helix formed by residues 87 - 100 (chain A) in PDB entry 1F16
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A THR 2.4 21.4 + - - -
86A ASP* 1.3 72.9 - - - +
88A PRO* 1.3 64.5 - - - +
89A ARG* 3.0 9.0 + - - +
90A GLU* 3.3 23.9 + - - +
91A VAL* 3.2 24.4 + - - +
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Residues in contact with PRO 88 (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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85A THR* 3.5 24.2 - - - +
86A ASP 3.5 8.5 - - - +
87A SER* 1.3 88.4 - - - +
89A ARG* 1.3 60.4 + - + +
91A VAL* 4.5 7.0 - - + -
92A PHE* 2.8 32.3 + - - +
120A LEU* 4.0 27.8 - - + +
132A LEU* 5.7 10.1 - - + -
139A TRP* 4.5 15.8 - - + -
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Residues in contact with ARG 89 (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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87A SER* 3.0 3.7 - - - +
88A PRO* 1.3 80.2 - - + +
90A GLU* 1.3 72.9 + - + +
92A PHE* 3.7 5.0 - - - +
93A PHE* 3.1 24.4 + - - +
139A TRP* 3.3 42.6 - - + +
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Residues in contact with GLU 90 (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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87A SER* 3.3 22.5 + - - +
89A ARG* 1.3 83.1 + - + +
91A VAL* 1.3 59.9 + - + +
93A PHE* 3.3 4.2 + - - +
94A ARG* 2.7 35.4 + - + +
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Residues in contact with VAL 91 (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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83A VAL* 4.9 9.0 - - + -
84A ASP 5.1 5.2 - - - +
85A THR 4.6 7.0 - - - +
87A SER* 3.2 26.1 + - - +
88A PRO* 4.4 5.6 - - + +
90A GLU* 1.3 79.0 - - + +
92A PHE* 1.3 59.0 + - - +
94A ARG* 4.3 5.8 - - - -
95A VAL* 2.7 55.0 + - + +
116A PHE* 4.8 10.3 - - + -
188A TRP* 3.8 30.7 - - + +
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Residues in contact with PHE 92 (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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88A PRO 2.8 23.1 + - - +
89A ARG* 3.7 5.6 - - - +
91A VAL* 1.3 78.4 - - - +
93A PHE* 1.3 68.1 + + + +
95A VAL* 4.6 0.2 - - - +
96A ALA* 2.9 33.0 + - + +
113A LEU* 4.4 24.9 - - + -
116A PHE* 4.2 16.1 - + - -
117A ALA* 4.8 11.9 - - + -
120A LEU* 4.0 25.1 - - + -
136A ILE* 6.2 1.6 - - + -
139A TRP* 3.7 51.1 - + + -
140A THR* 4.5 8.3 - - + -
143A PHE* 4.8 15.5 - + + -
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Residues in contact with PHE 93 (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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89A ARG 3.1 14.3 + - - +
90A GLU* 4.0 4.0 - - - +
92A PHE* 1.3 87.0 - + + +
94A ARG* 1.3 67.5 + - - +
96A ALA* 3.8 2.0 - - - +
97A ALA* 3.0 33.4 + - + +
143A PHE* 5.2 19.3 - + - -
147A ARG* 6.2 2.9 - - - -
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Residues in contact with ARG 94 (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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90A GLU* 2.7 25.9 + - + +
91A VAL* 4.0 4.0 - - - +
93A PHE* 1.3 76.7 - - - +
95A VAL* 1.3 71.9 + - + +
97A ALA* 3.7 5.0 - - - +
98A ASP* 3.2 43.6 + - - +
184A SER* 5.3 1.8 + - - +
187A ILE* 4.6 17.4 + - - +
188A TRP* 4.6 30.1 - - + +
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Residues in contact with VAL 95 (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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83A VAL* 6.4 0.2 - - + -
91A VAL* 2.7 45.4 + - + +
92A PHE 4.6 0.9 - - - +
94A ARG* 1.3 76.5 - - - +
96A ALA* 1.3 66.1 + - - +
98A ASP* 3.1 17.8 + - - +
99A MET* 3.3 22.4 + - + +
116A PHE* 4.6 23.6 - - + -
181A LEU* 5.6 1.3 - - + -
184A SER* 4.2 21.3 + - - -
185A LEU* 5.5 8.1 - - + -
188A TRP* 3.7 23.6 - - + +
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Residues in contact with ALA 96 (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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92A PHE* 2.9 27.6 + - + +
93A PHE* 3.8 5.4 - - - +
95A VAL* 1.3 79.4 - - - +
97A ALA* 1.3 56.1 + - - +
99A MET* 2.5 44.9 + - - +
100A PHE* 3.3 10.7 - - + -
113A LEU* 5.1 14.6 - - + -
116A PHE* 6.1 0.4 - - - -
143A PHE* 4.4 21.5 - - + -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.0 33.7 + - + +
94A ARG* 3.7 5.6 - - - +
96A ALA* 1.3 78.1 - - - +
98A ASP* 1.3 57.2 + - - +
100A PHE* 3.1 9.0 + - - +
101A SER* 2.7 30.6 + - - -
143A PHE* 5.1 6.7 - - - -
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Residues in contact with ASP 98 (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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94A ARG* 3.2 25.2 + - - +
95A VAL* 3.1 13.7 + - - +
96A ALA 2.7 4.6 + - - -
97A ALA* 1.3 78.1 - - - +
99A MET* 1.3 62.3 + - - +
100A PHE 3.2 0.3 + - - -
101A SER* 3.2 20.3 + - - -
102A ASP* 4.1 7.4 - - - +
184A SER* 3.4 20.9 + - - +
187A ILE* 3.7 27.7 - - - +
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Residues in contact with MET 99 (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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95A VAL* 3.8 27.1 - - + +
96A ALA* 2.5 21.8 + - - +
98A ASP* 1.3 74.1 - - - +
100A PHE* 1.3 71.8 + - + -
101A SER 3.9 0.2 + - - -
102A ASP* 4.8 7.1 - - - +
109A ARG* 4.1 37.7 - - + +
112A ALA* 4.0 23.3 - - + +
113A LEU* 4.7 7.6 - - + -
116A PHE* 5.0 7.0 - - + -
180A VAL* 5.5 11.7 - - + -
181A LEU* 3.6 32.3 - - + -
184A SER* 4.2 13.0 - - - +
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Residues in contact with PHE 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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96A ALA* 3.3 17.0 - - + -
97A ALA* 3.1 6.6 + - - +
98A ASP 3.1 0.2 - - - -
99A MET* 1.3 93.9 - - + +
101A SER* 1.3 57.9 + - - +
102A ASP 2.9 20.0 + - - +
103A GLY 5.1 0.7 - - - +
104A ASN* 4.8 4.5 - - - +
109A ARG* 3.2 65.1 - - + +
110A VAL 4.8 0.7 - - - -
113A LEU* 4.9 11.0 - - + -
143A PHE* 3.9 33.7 - + + -
147A ARG* 6.1 5.6 - - + +
148A LEU* 4.0 17.9 - - + -
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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