Contacts of the helix formed by residues 101 - 117 (chain A) in PDB entry 3RLG
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 GLN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ASP 3.1 42.3 + - - +
40A ALA* 3.8 7.7 - - + +
97A LEU* 3.6 19.2 - - + +
98A TYR* 2.9 48.1 + - + +
100A ASN* 1.4 87.0 - - - +
102A ALA* 1.3 59.6 + - - +
103A ASN 3.4 2.5 - - - -
104A ASP* 3.3 17.7 + - - +
105A ALA* 2.8 30.3 + - - +
291A EDO 3.9 17.4 - - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 6.0 1.3 - - - -
97A LEU* 5.3 2.7 - - - -
98A TYR 4.0 2.2 + - - -
99A ASP 3.3 14.5 + - - +
100A ASN 3.5 0.8 - - - -
101A GLN* 1.3 78.1 - - - +
103A ASN* 1.3 63.9 + - - +
105A ALA* 3.2 7.8 + - - +
106A GLY 3.1 17.5 + - - -
137A ASN 5.1 0.2 - - - +
138A HIS* 3.8 45.1 - - + +
140A PRO* 4.6 6.7 - - + -
141A LEU* 3.2 18.8 - - + +
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Residues in contact with ASN 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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100A ASN 5.2 3.5 + - - +
101A GLN 3.4 0.2 - - - -
102A ALA* 1.3 76.9 - - - +
104A ASP* 1.3 68.0 + - - +
106A GLY* 3.0 12.0 + - - -
107A LYS* 3.1 40.3 + - - +
140A PRO* 3.3 27.4 + - + +
141A LEU* 4.0 1.2 - - - +
143A LYS* 4.0 13.7 - - - +
144A GLY* 3.3 26.0 - - - +
147A ASP* 5.4 0.8 + - - -
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Residues in contact with ASP 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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39A ASN 4.9 1.9 - - - +
40A ALA* 4.1 10.6 - - + +
100A ASN 4.4 5.4 + - - +
101A GLN* 3.3 26.8 + - - +
103A ASN* 1.3 80.8 - - - +
105A ALA* 1.3 63.5 + - - +
107A LYS* 3.2 9.5 + - - +
108A LYS* 2.9 27.9 + - + +
289A PGE 3.6 41.1 - - - +
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Residues in contact with ALA 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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37A PHE* 3.8 20.9 - - + -
40A ALA* 3.4 14.2 - - + +
94A THR* 5.0 0.4 - - + -
97A LEU* 3.8 17.7 - - + -
101A GLN 2.8 16.9 + - - +
102A ALA* 3.2 10.5 + - - +
104A ASP* 1.3 73.7 - - - +
106A GLY* 1.4 57.5 + - - +
108A LYS* 3.8 1.2 - - - +
109A LEU* 3.0 34.7 + - - +
141A LEU* 4.1 11.0 - - + -
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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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102A ALA 3.1 7.5 + - - -
103A ASN 3.0 5.7 + - - -
105A ALA* 1.4 75.2 - - - +
107A LYS* 1.3 57.8 + - - +
109A LEU* 3.4 2.4 + - - -
110A ALA 2.9 24.1 + - - -
141A LEU* 3.4 37.4 - - - +
145A PHE* 3.3 20.8 - - - -
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Residues in contact with LYS 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 ASN* 3.1 31.6 + - - +
104A ASP* 3.5 11.2 + - - +
106A GLY* 1.3 77.2 - - - +
108A LYS* 1.4 58.0 + - - +
110A ALA 3.2 0.9 + - - -
111A LYS* 3.0 33.8 + - - +
144A GLY* 3.3 23.8 - - - +
147A ASP* 5.1 10.5 - - - -
148A GLN* 3.5 26.4 - - + +
289A PGE 3.7 30.3 - - - -
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Residues in contact with LYS 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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39A ASN 4.1 4.9 - - - -
40A ALA 3.4 25.4 - - - +
41A ASN* 3.4 18.3 - - - +
42A PRO* 3.6 4.7 - - + -
104A ASP* 2.9 19.2 + - - +
105A ALA 3.9 0.2 - - - +
107A LYS* 1.4 74.7 - - - +
109A LEU* 1.3 57.7 + - - +
111A LYS* 3.3 8.2 + - + +
112A ASN* 3.0 32.7 + - - -
288A PEG 2.8 40.5 + - - +
289A PGE 2.9 73.4 + - - +
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Residues in contact with LEU 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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35A VAL* 4.2 1.8 - - + -
37A PHE* 3.8 13.0 - - + -
42A PRO* 3.5 28.0 - - + +
63A PHE* 4.1 19.7 - - + -
90A PHE* 5.9 1.3 - - + -
92A LEU* 3.6 45.5 - - + -
105A ALA 3.0 21.9 + - - +
106A GLY 3.5 4.3 - - - +
108A LYS* 1.3 72.7 - - - +
110A ALA* 1.4 60.3 + - - +
112A ASN* 3.2 3.0 + - - +
113A LEU* 2.9 38.4 + - + +
131A LEU* 5.1 4.0 - - + -
141A LEU* 4.1 13.7 - - + -
145A PHE* 3.9 12.3 - - + -
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Residues in contact with ALA 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 GLY 2.9 15.7 + - - +
107A LYS 3.6 4.5 - - - +
109A LEU* 1.4 75.4 - - - +
111A LYS* 1.3 58.5 + - - +
113A LEU* 4.0 0.8 - - - +
114A LEU* 2.8 33.1 + - - +
145A PHE* 3.5 41.9 - - + +
148A GLN* 3.7 12.1 - - + -
149A LEU* 4.1 13.7 - - + +
152A ASP* 5.5 0.2 - - - -
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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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107A LYS 3.0 18.0 + - - +
108A LYS* 3.6 10.3 - - + +
109A LEU 3.3 0.2 - - - -
110A ALA* 1.3 74.7 - - - +
112A ASN* 1.3 68.1 + - - +
114A LEU* 3.8 4.9 - - - +
115A GLN* 3.0 26.2 + - - +
148A GLN* 3.6 28.2 - - + +
151A LYS* 5.7 2.6 - - - +
152A ASP* 4.3 13.8 + - - +
288A PEG 4.2 15.7 - - - +
289A PGE 3.5 26.7 + - - +
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Residues in contact with ASN 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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41A ASN* 3.9 13.1 + - - +
42A PRO* 3.3 32.4 - - - +
63A PHE* 3.5 15.5 - - + -
64A ASN* 3.2 35.2 + - - +
67A LEU* 3.5 1.9 - - + +
108A LYS 3.0 15.0 + - - +
109A LEU 3.7 6.3 - - - +
111A LYS* 1.3 82.1 - - - +
113A LEU* 1.3 63.5 + - - +
115A GLN* 4.7 0.2 - - - -
116A HIS* 2.9 34.4 + - - +
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Residues in contact with LEU 113 (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 PHE* 4.8 3.4 - - + -
67A LEU* 3.6 32.3 - - + -
90A PHE* 3.8 22.7 - - + -
109A LEU* 2.9 30.2 + - + +
110A ALA 4.0 1.6 - - - +
112A ASN* 1.3 78.0 - - - +
114A LEU* 1.3 61.3 + - - +
117A TYR* 2.9 24.5 + - + +
118A TRP* 2.8 48.2 + - + -
129A ILE* 5.0 4.5 - - + -
131A LEU* 4.6 9.9 - - + -
145A PHE* 3.5 26.0 - - + -
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Residues in contact with LEU 114 (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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110A ALA 2.8 20.0 + - - +
111A LYS* 3.8 4.3 - - - +
113A LEU* 1.3 77.0 - - - +
115A GLN* 1.3 58.8 + - - +
118A TRP* 3.8 8.1 - - + -
119A ASN 3.0 10.0 + - - -
120A ASN* 2.8 49.2 + - - +
149A LEU* 4.3 11.2 - - + -
152A ASP* 3.6 36.6 - - + +
154A HIS* 3.6 39.0 - - + +
157A LEU* 3.6 17.5 - - + -
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Residues in contact with GLN 115 (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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111A LYS 3.0 18.5 + - - +
112A ASN* 4.7 0.2 - - - -
114A LEU* 1.3 80.3 - - - +
116A HIS* 1.3 91.3 + - + +
119A ASN* 3.5 23.2 + - - +
120A ASN* 2.9 27.9 + - - +
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Residues in contact with HIS 116 (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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64A ASN* 3.2 49.7 + - + +
67A LEU* 3.8 24.2 - - + +
68A LYS* 3.9 30.6 - - + +
71A ARG* 3.7 21.3 + - - +
112A ASN* 2.9 20.9 + - - +
115A GLN* 1.3 100.9 + - + +
117A TYR* 1.3 63.1 + - - +
119A ASN* 4.4 1.3 - - - -
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Residues in contact with TYR 117 (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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67A LEU* 3.8 11.7 - - + -
70A LEU* 3.5 26.9 - - + -
71A ARG* 3.3 28.8 - - - +
74A THR* 2.7 29.6 + - - -
113A LEU* 2.9 34.8 + - + +
116A HIS* 1.3 80.6 - - - +
118A TRP* 1.3 82.2 + + - +
119A ASN 3.3 4.0 - - - -
125A GLY* 2.9 43.0 + - - -
127A ALA* 2.9 38.4 + - + +
129A ILE* 4.1 11.2 - - + -
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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