Contacts of the helix formed by residues 99 - 110 (chain A) in PDB entry 5FLM
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 PHE 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.7 34.1 - - + -
96A HIS* 3.2 23.1 + + + +
98A GLY* 1.3 73.7 - - - +
100A LEU* 1.3 57.7 + - - +
101A VAL 3.3 1.1 - - - -
102A LYS* 3.1 11.7 + - + +
103A THR* 2.9 28.3 + - - -
247A TRP 4.7 0.2 - - - -
248A MET* 3.6 45.8 - - + +
1440A MET* 3.4 49.4 - - + -
1443A ALA* 4.6 1.6 - - + -
1444A ALA* 4.3 10.8 - - + -
1166B SER* 3.8 19.1 - - - -
1167B ILE* 4.3 15.5 - - + -
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Residues in contact with LEU 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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95A PHE* 3.9 36.3 - - + -
96A HIS 3.0 10.1 + - - +
97A VAL* 3.3 20.2 - - + +
98A GLY 3.1 2.0 - - - -
99A PHE* 1.3 76.7 - - - +
101A VAL* 1.3 61.1 + - + +
103A THR* 3.2 10.1 + - - -
104A MET* 2.9 30.8 + - - +
193A ARG* 3.6 35.0 - - + +
195A GLY 4.6 1.3 - - - +
196A LEU* 4.3 26.9 - - + +
198A LEU* 4.5 18.6 - - + -
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Residues in contact with VAL 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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97A VAL 5.7 1.3 - - - +
98A GLY 4.1 7.3 + - - +
99A PHE 3.3 0.4 - - - -
100A LEU* 1.3 79.5 - - + +
102A LYS* 1.3 68.0 + - + +
104A MET* 3.1 15.3 + - + +
105A LYS* 2.9 46.4 + - + +
193A ARG* 5.6 8.3 - - - +
32N T 5.8 2.5 - - - +
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Residues in contact with LYS 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 GLY 5.3 2.0 - - - +
99A PHE* 3.1 16.0 + - + +
101A VAL* 1.3 79.9 - - + +
103A THR* 1.3 63.6 + - - +
105A LYS* 3.3 13.7 + - + +
106A VAL* 2.9 33.2 + - + +
138A LYS* 5.1 0.2 - - - +
141A LEU* 3.3 28.9 - - - +
238A MET* 5.3 4.0 - - - -
248A MET* 3.6 18.4 - - + -
1440A MET 5.4 1.6 - - - +
1441A GLU* 2.7 42.9 + - - +
1444A ALA* 4.1 20.4 - - + -
1445A HIS* 3.0 24.6 + - - -
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Residues in contact with THR 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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95A PHE* 5.0 9.2 - - + -
99A PHE* 2.9 18.9 + - - +
100A LEU* 3.3 14.8 - - + -
102A LYS* 1.3 76.3 - - - +
104A MET* 1.3 56.9 + - - +
106A VAL 3.8 0.3 - - - -
107A LEU* 2.9 41.9 + - + +
198A LEU* 4.7 9.4 - - + -
221A VAL* 3.8 16.2 - - + -
225A PHE* 3.8 27.1 - - + -
248A MET* 4.0 23.6 + - - +
249A ILE* 5.1 2.9 - - + +
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Residues in contact with MET 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 LEU* 2.9 17.6 + - + +
101A VAL* 3.1 14.8 + - + +
103A THR* 1.3 76.7 - - - +
105A LYS* 1.3 61.9 + - + +
107A LEU* 3.2 8.5 + - - +
108A ARG* 2.9 56.6 + - - +
191A ILE* 4.0 15.4 - - + +
193A ARG* 3.6 52.5 - - + +
198A LEU* 3.8 23.1 - - + -
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Residues in contact with LYS 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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101A VAL* 2.9 37.3 + - + +
102A LYS* 3.8 17.7 - - + +
104A MET* 1.3 75.5 - - + +
106A VAL* 1.3 57.7 + - + +
108A ARG* 3.0 4.4 + - - +
109A CYS* 2.9 33.9 + - - -
138A LYS* 5.6 6.3 - - - +
141A LEU* 3.8 31.1 - - + +
142A THR* 5.0 11.3 - - - +
145A TYR* 4.0 36.6 - - + +
1441A GLU* 5.3 3.4 + - - -
32N T 4.8 13.0 + - - -
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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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102A LYS* 2.9 25.2 + - + +
103A THR 4.0 2.5 - - - +
105A LYS* 1.3 75.7 - - + +
107A LEU* 1.3 62.5 + - - +
109A CYS* 3.2 7.0 + - - -
110A VAL* 3.1 23.8 + - + +
141A LEU* 4.8 12.8 - - + -
225A PHE* 3.7 24.5 - - + -
228A ILE* 4.1 11.9 - - + -
236A LEU* 3.8 24.5 - - + -
238A MET* 3.6 24.7 - - + -
245A PRO* 4.2 6.1 - - + -
248A MET* 4.5 4.3 - - + -
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Residues in contact with LEU 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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103A THR* 2.9 38.5 + - + +
104A MET* 3.5 6.1 - - - +
105A LYS 3.2 0.2 - - - -
106A VAL* 1.3 78.3 - - - +
108A ARG* 1.3 57.4 + - - +
110A VAL* 2.8 27.7 - - - +
112A PHE* 4.1 22.3 - - + -
191A ILE* 3.5 27.4 - - + +
198A LEU* 4.0 20.2 - - + -
216A LEU* 4.1 8.7 - - + -
221A VAL* 3.7 14.6 - - + -
224A ILE* 4.4 14.6 - - + -
225A PHE* 3.7 23.3 - - + -
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Residues in contact with ARG 108 (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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104A MET* 2.9 36.9 + - - +
105A LYS* 3.0 7.8 + - - +
107A LEU* 1.3 75.3 - - - +
109A CYS* 1.3 57.6 + - - +
110A VAL 3.4 0.2 - - - -
118A LEU* 3.3 21.2 - - - +
145A TYR* 2.7 47.3 + - + -
148A CYS 3.7 9.7 - - - +
149A LYS* 4.7 7.2 + - + +
190A ARG* 5.3 6.2 - - - +
191A ILE* 3.1 43.8 + - + +
192A ARG* 5.3 0.8 - - - +
33N T 4.2 27.3 + - - -
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Residues in contact with CYS 109 (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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105A LYS* 2.9 21.1 + - - +
106A VAL* 3.8 4.3 - - - +
107A LEU 3.2 0.4 - - - -
108A ARG* 1.3 77.3 - - - +
110A VAL* 1.3 62.3 + - - +
117A LEU* 3.7 9.4 - - - +
118A LEU* 3.5 22.1 + - - -
141A LEU* 5.0 3.1 - - - -
144A VAL* 4.1 4.9 - - - -
145A TYR* 3.5 43.1 - - - -
148A CYS* 3.8 14.9 - - + -
236A LEU* 3.7 28.3 - - + -
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Residues in contact with VAL 110 (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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106A VAL 3.1 18.5 + - - +
107A LEU* 2.8 19.4 + - - +
108A ARG 3.4 0.6 - - - -
109A CYS* 1.3 84.1 - - - +
111A CYS* 1.3 68.3 + - - +
112A PHE* 3.7 6.6 + - - -
115A SER* 3.3 37.7 - - - +
116A LYS 4.1 2.9 - - - -
117A LEU* 4.3 7.4 - - + -
118A LEU* 4.3 4.8 - - - +
188A GLN* 4.3 2.6 - - - +
224A ILE* 4.4 12.1 - - + +
225A PHE* 5.8 0.7 - - + -
228A ILE* 4.1 25.6 - - + -
236A LEU* 4.1 16.8 - - + -
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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