Contacts of the helix formed by residues 99 - 112 (chain A) in PDB entry 3RU0
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 PRO 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TYR 4.5 0.7 - - - +
98A PRO* 1.3 92.0 - - + +
100A ASP* 1.3 66.7 + - - +
101A SER* 4.2 14.4 - - - +
102A VAL* 3.0 15.3 + - + +
103A ARG* 3.2 9.5 + - - +
147A LEU* 4.1 20.2 - - + -
150A THR* 3.8 20.9 - - + +
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Residues in contact with ASP 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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39A THR* 3.8 4.6 - - + +
40A VAL 4.3 3.3 - - - +
41A CYS* 3.4 17.9 - - - +
42A LYS* 3.2 43.2 + - - +
97A TYR* 4.3 11.1 + - - -
98A PRO 4.6 0.6 - - - +
99A PRO* 1.3 71.9 - - - +
101A SER* 1.3 51.8 + - - +
103A ARG* 3.3 7.8 + - - +
104A LEU* 2.8 35.9 + - - +
195A VAL* 4.0 19.6 - - + +
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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
----------------------------------------------------------
99A PRO* 4.2 4.7 - - - +
100A ASP* 1.3 79.1 - - - +
102A VAL* 1.3 58.0 + - - +
104A LEU* 3.5 9.0 - - - +
105A LEU* 2.9 34.1 + - - +
147A LEU* 3.8 18.4 - - - +
175A PHE* 3.6 20.1 - - - -
178A VAL* 3.9 25.8 - - - -
195A VAL* 5.8 0.2 - - - -
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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
----------------------------------------------------------
98A PRO* 3.7 19.7 - - + -
99A PRO* 3.0 26.5 + - + +
101A SER* 1.3 73.2 + - - +
103A ARG* 1.3 60.5 + - - +
105A LEU* 3.3 1.0 + - - -
106A GLY* 2.9 27.7 + - - -
147A LEU* 4.1 14.4 - - + +
150A THR* 4.0 11.2 - - + -
151A PHE* 3.9 23.3 - - + +
154A PHE* 3.8 20.4 - - + -
175A PHE* 3.7 28.3 - - + -
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Residues in contact with ARG 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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39A THR* 3.3 27.3 + - + +
40A VAL* 3.9 12.7 - - - +
45A ARG* 4.7 4.0 - - - +
50A ASP* 2.8 26.8 + - - -
67A VAL* 4.8 3.2 + - - +
68A ALA* 4.5 4.2 - - - +
83A HIS* 4.4 2.2 + - - -
86A GLU* 2.8 40.8 + - - +
90A LEU* 3.8 25.8 - - + +
97A TYR* 2.9 38.1 + - + +
98A PRO* 4.4 8.7 - - + +
99A PRO 3.2 8.5 + - - +
100A ASP* 3.7 9.0 - - - +
102A VAL* 1.3 78.6 - - - +
104A LEU* 1.3 61.2 + - - +
106A GLY* 3.4 2.4 + - - -
107A ARG* 3.2 29.2 + - - +
154A PHE* 4.6 11.7 - - + -
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Residues in contact with LEU 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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37A ALA* 3.5 31.6 - - + +
38A TYR* 3.6 17.9 - - - +
39A THR* 4.0 10.0 - - + +
100A ASP 2.8 21.0 + - - +
101A SER* 3.5 5.8 - - - +
103A ARG* 1.3 72.7 - - - +
105A LEU* 1.3 58.4 + - - +
107A ARG* 3.1 9.8 + - + +
108A VAL* 3.0 28.9 + - + +
178A VAL* 4.3 22.7 - - + -
182A SER* 4.5 0.2 - - - +
195A VAL* 4.0 26.5 - - + +
196A GLY* 4.1 1.6 - - - -
197A LEU* 3.9 29.2 - - + +
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Residues in contact with LEU 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 2.9 17.8 + - - +
102A VAL 4.1 2.2 - - - +
104A LEU* 1.3 70.6 - - + +
106A GLY* 1.3 65.2 + - - +
108A VAL* 3.6 22.2 - - + +
109A VAL* 3.1 31.2 + - + +
126A PHE* 4.3 9.2 - - + -
151A PHE* 3.8 13.9 - - + -
169A PHE* 4.6 3.1 - - + -
171A LEU* 4.7 3.1 - - + -
174A ALA* 3.8 22.0 - - + +
175A PHE* 3.6 58.1 - - + +
178A VAL* 3.8 22.2 - - + -
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Residues in contact with GLY 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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86A GLU* 6.0 4.7 - - - -
102A VAL 2.9 17.6 + - - -
103A ARG* 3.6 4.3 - - - -
104A LEU 3.2 0.4 - - - -
105A LEU* 1.3 75.2 - - - +
107A ARG* 1.3 58.8 + - - +
109A VAL* 3.4 6.5 - - - +
110A PHE* 3.3 26.3 - - - -
151A PHE* 3.6 13.7 - - - -
154A PHE* 5.7 0.7 - - - -
155A MET* 4.0 17.7 - - - -
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Residues in contact with ARG 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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37A ALA* 4.1 12.6 - - + +
38A TYR* 2.8 46.9 + - - +
39A THR* 4.5 8.7 - - - +
50A ASP* 4.2 12.5 + - - +
70A TYR* 5.5 1.0 + - - -
79A ALA* 5.4 3.8 + - - +
82A ASP* 3.7 53.8 + - + +
83A HIS* 4.6 4.8 + - - +
86A GLU* 2.9 40.0 + - + +
103A ARG* 3.2 26.5 + - - +
104A LEU 3.1 9.2 + - - +
106A GLY* 1.3 75.8 - - - +
108A VAL* 1.3 64.3 + - - +
109A VAL 3.2 0.7 + - - -
110A PHE* 3.4 8.3 + - - +
111A LYS* 3.3 18.8 + - - +
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Residues in contact with VAL 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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36A LEU* 4.6 7.2 - - + -
37A ALA* 3.5 26.2 - - + -
104A LEU* 3.0 17.3 + - + +
105A LEU* 3.1 19.4 + - + +
107A ARG* 1.3 74.7 - - - +
109A VAL* 1.3 64.3 + - - +
111A LYS* 3.0 6.9 + - - +
112A LEU* 3.0 45.5 + - + +
126A PHE* 4.0 21.5 - - + -
169A PHE* 4.8 1.6 - - + -
197A LEU* 3.7 24.9 - - + -
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Residues in contact with VAL 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 LEU 3.1 12.3 + - - +
106A GLY* 3.4 17.9 - - - +
108A VAL* 1.3 75.4 - - - +
110A PHE* 1.3 72.3 + - + +
112A LEU* 3.7 15.9 + - - +
113A MET* 3.6 20.9 - - - +
151A PHE* 4.2 8.5 - - + -
159A ILE* 4.0 8.7 - - + -
165A LEU* 3.9 28.9 - - + -
166A PRO* 4.2 5.0 - - + +
169A PHE* 3.3 42.8 - - + -
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Residues in contact with PHE 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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85A ARG* 3.5 66.6 - - + +
106A GLY 3.3 26.7 - - - -
107A ARG* 3.4 5.9 + - - +
108A VAL 3.2 0.2 - - - -
109A VAL* 1.3 76.3 - - + +
111A LYS* 1.3 64.8 - - - +
112A LEU 3.2 0.2 - - - -
113A MET* 3.2 41.4 + - + +
114A ASP* 3.9 3.6 + - - +
155A MET* 3.6 17.0 - - + -
158A GLU* 4.3 2.2 - - + -
159A ILE* 3.5 32.8 - - + -
164A GLN 5.7 0.4 - - - -
165A LEU* 4.4 1.6 - - + -
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Residues in contact with LYS 111 (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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35A PRO 4.5 6.1 + - - -
36A LEU* 3.3 54.7 + - + +
37A ALA* 5.3 0.7 - - + -
82A ASP* 5.5 6.9 + - - +
107A ARG 3.3 11.5 + - - +
108A VAL* 3.0 14.6 + - - +
110A PHE* 1.3 79.0 - - - +
112A LEU* 1.3 60.6 + - - +
114A ASP* 3.1 30.0 + - + +
118A SER* 4.3 16.2 + - - -
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Residues in contact with LEU 112 (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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36A LEU* 4.5 8.7 - - + -
108A VAL* 3.0 34.8 + - + +
109A VAL* 3.7 11.4 - - - +
110A PHE 3.2 0.4 - - - -
111A LYS* 1.3 74.9 - - - +
113A MET* 1.3 60.8 + - - +
114A ASP 3.4 5.3 - - - +
121A GLU* 4.4 9.6 - - - +
126A PHE* 3.8 31.9 - - + -
127A TYR* 3.8 31.4 + - + +
166A PRO* 4.5 9.7 - - + +
169A PHE* 3.7 29.2 - - + -
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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