Contacts of the helix formed by residues 100 - 109 (chain A) in PDB entry 5UFL
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 ASN 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 5.3 1.0 - - - +
94A GLN* 5.2 10.0 + - - +
99A LEU* 1.3 77.9 - - - +
101A SER* 1.3 56.4 + - - +
103A LEU* 4.2 5.9 - - - +
104A ALA* 3.0 31.2 + - - +
124A LEU* 4.5 10.4 - - + +
127A LEU* 3.3 36.6 + - - +
128A THR* 3.6 30.7 - - + +
131A VAL* 4.8 8.3 - - - +
133A ILE* 5.2 7.5 - - + +
134A PHE* 4.3 17.9 - - + -
140A ILE* 4.6 6.4 - - + +
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Residues in contact with SER 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 LEU 3.2 4.1 - - - +
100A ASN* 1.3 81.3 - - - +
102A VAL* 1.3 65.5 + - - +
104A ALA* 3.6 12.1 - - - +
105A GLY* 3.6 5.0 + - - -
134A PHE* 4.1 14.2 - - - -
138A ALA* 3.2 43.9 + - - +
139A ASN* 4.1 6.9 - - - +
140A ILE* 5.0 0.4 - - - -
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Residues in contact with VAL 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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60A VAL* 3.7 18.2 - - + -
63A LEU* 3.9 12.3 - - + +
64A GLU* 3.2 41.8 - - + +
96A THR 5.0 6.3 - - - +
99A LEU* 3.3 31.8 - - + +
101A SER* 1.3 81.0 - - - +
103A LEU* 1.3 67.3 + - - +
104A ALA 3.3 0.4 - - - -
105A GLY* 3.2 12.0 + - - +
106A VAL* 3.5 14.2 + - - +
109A ARG* 5.4 0.5 + - - -
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Residues in contact with LEU 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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63A LEU* 4.5 11.4 - - + -
77A ILE* 4.5 20.0 - - + -
80A LEU* 5.0 4.3 - - + -
99A LEU* 2.8 49.8 + - + +
100A ASN* 4.2 3.1 - - - +
102A VAL* 1.3 70.8 - - - +
104A ALA* 1.3 63.3 + - - +
106A VAL* 3.3 27.0 + - + +
107A VAL* 3.9 2.6 + - - +
120A CYS* 3.8 29.3 - - - +
123A LEU* 4.4 11.9 - - + -
124A LEU* 3.8 25.0 - - + +
127A LEU* 3.9 20.6 - - + -
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Residues in contact with ALA 104 (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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100A ASN 3.0 20.5 + - - +
101A SER 3.6 6.7 - - - +
103A LEU* 1.3 76.4 - - - +
105A GLY* 1.3 56.5 + - - +
107A VAL* 3.2 26.7 - - - +
108A CYS* 3.3 11.3 - - - -
124A LEU* 4.4 8.4 - - + +
139A ASN* 3.5 24.9 - - - +
140A ILE* 4.3 7.2 - - + -
143A LEU* 4.3 19.1 - - + +
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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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101A SER 3.6 3.6 + - - -
102A VAL* 3.2 11.3 + - - -
104A ALA* 1.3 77.4 - - - +
106A VAL* 1.3 61.1 + - - +
108A CYS* 3.6 3.6 + - - +
109A ARG* 3.2 37.8 + - - +
139A ASN* 3.4 18.8 - - - +
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Residues in contact with VAL 106 (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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63A LEU* 3.9 24.2 - - + +
73A ILE* 5.2 14.4 - - + -
102A VAL 3.6 14.8 - - - +
103A LEU* 3.5 17.3 - - + +
104A ALA 3.3 1.0 - - - -
105A GLY* 1.3 74.2 - - - +
107A VAL* 1.3 60.1 + - - +
109A ARG* 3.0 48.0 + - - +
116A VAL* 5.1 19.4 - - + +
117A PHE* 5.0 1.4 - - - -
120A CYS* 4.0 16.6 - - + -
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Residues in contact with VAL 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 LEU 3.9 1.5 + - - +
104A ALA* 3.2 20.2 - - - +
106A VAL* 1.3 77.1 - - + +
108A CYS* 1.3 64.8 + - - +
109A ARG 4.0 1.4 - - - +
117A PHE* 3.4 38.0 - - + -
120A CYS* 3.6 32.3 - - + -
121A ILE* 4.2 18.2 - - + -
124A LEU* 5.4 1.6 - - + -
143A LEU* 3.8 26.0 - - + -
146A PHE* 4.1 26.5 - - + -
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Residues in contact with CYS 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 ALA 3.3 18.2 - - - -
105A GLY* 3.8 7.0 - - - +
106A VAL 3.2 0.6 - - - -
107A VAL* 1.3 84.0 - - - +
109A ARG* 1.3 66.2 + - + +
139A ASN* 3.8 9.2 - - - +
142A GLU* 3.6 46.4 - - + +
143A LEU* 4.7 1.6 - - - -
146A PHE* 5.8 4.9 - - - -
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Residues in contact with ARG 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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63A LEU 3.0 26.7 + - - -
64A GLU* 4.8 6.4 + - - +
65A ASP 4.8 2.8 - - - +
66A PRO* 3.7 42.0 - - + +
73A ILE* 6.3 1.4 - - - +
102A VAL 5.4 0.2 + - - -
105A GLY* 3.2 17.9 + - - +
106A VAL* 3.0 41.4 + - - +
107A VAL 4.0 3.8 - - - +
108A CYS* 1.3 81.4 - - + +
113A THR* 4.9 11.7 + - - -
117A PHE* 5.1 3.6 - - - -
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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