Contacts of the helix formed by residues 111 - 126 (chain A) in PDB entry 6G2T
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.4 26.9 - - + -
109A LEU 4.0 4.0 - - - +
110A ASN* 1.3 109.1 - - - +
112A LYS* 1.3 65.6 + - - +
113A ALA* 3.3 7.4 + - + +
114A ASN* 3.4 10.9 + - - +
115A ARG* 4.1 4.5 + - - +
176A ARG* 4.1 5.2 - - - +
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Residues in contact with LYS 112 (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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110A ASN 3.7 2.0 + - - +
111A PRO* 1.3 70.5 - - - +
113A ALA* 1.3 65.8 + - - +
115A ARG 3.3 10.0 + - - -
116A GLU* 3.3 24.1 + - - +
370A HIS* 3.4 57.5 + - + +
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Residues in contact with ALA 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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78A TRP* 4.9 1.1 - - - -
111A PRO* 3.3 5.6 - - + +
112A LYS* 1.3 77.7 - - - +
114A ASN* 1.3 65.8 + - - +
116A GLU* 3.4 9.1 + - - +
117A LYS* 3.1 27.7 + - - +
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Residues in contact with ASN 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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73A GLY 3.8 1.6 + - - -
74A ILE* 3.1 41.5 - - - +
75A VAL* 3.5 24.3 + - + +
78A TRP* 3.4 16.2 + - + -
106A GLU* 4.2 8.5 - - - +
110A ASN* 3.1 28.9 + - - +
111A PRO* 3.4 5.8 + - - +
112A LYS 3.3 1.0 - - - -
113A ALA* 1.3 78.5 - - - +
115A ARG* 1.3 57.6 + - - +
118A MET* 3.1 33.3 + - + +
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Residues in contact with ARG 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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106A GLU* 3.2 50.0 + - + +
107A ALA 3.8 10.9 + - - -
108A PRO* 4.8 1.6 - - - +
109A LEU 4.9 1.6 - - - +
110A ASN* 4.0 19.8 + - - +
111A PRO 4.1 4.0 + - - +
112A LYS 3.3 8.6 + - - +
114A ASN* 1.3 77.6 - - - +
116A GLU* 1.3 62.6 + - - +
118A MET* 3.5 5.6 + - - +
119A THR* 3.3 28.8 + - - +
133A VAL* 5.1 7.9 - - + +
135A ILE* 4.0 16.6 - - - +
369A VAL* 3.9 22.2 - - + -
370A HIS* 3.5 33.2 + - + +
373A CYS* 6.4 0.2 - - - -
374A PHE* 4.3 25.2 + - - -
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Residues in contact with GLU 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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112A LYS* 3.3 26.6 + - - +
113A ALA* 4.0 7.6 - - - +
115A ARG* 1.3 76.7 - - - +
117A LYS* 1.3 60.6 + - - +
119A THR* 2.9 20.1 + - - -
120A GLN* 3.1 14.3 + - - +
366A PRO* 3.9 29.0 - - + +
367A SER* 3.7 23.9 - - - +
369A VAL* 4.6 1.8 - - + -
370A HIS* 3.9 22.0 - - + -
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Residues in contact with LYS 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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78A TRP* 3.3 52.9 - - + +
113A ALA 3.1 11.5 + - - +
116A GLU* 1.3 75.7 - - - +
118A MET* 1.3 60.2 - - - +
120A GLN* 3.1 35.6 + - - +
121A ILE* 2.8 50.2 + - + +
201G SER* 3.7 25.4 + - - +
202G LYS* 4.0 14.3 - - - +
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Residues in contact with MET 118 (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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11A ASN* 6.0 6.7 - - + -
70A ILE* 6.6 0.2 - - + -
75A VAL* 5.6 9.2 - - + -
78A TRP* 3.8 17.2 - - + -
85A TRP* 3.7 26.1 - - + -
104A LEU* 3.8 33.4 - - + -
105A THR 5.0 11.2 - - - +
106A GLU* 4.3 18.8 - - - +
114A ASN* 3.1 28.3 + - + +
115A ARG* 3.7 5.6 - - - +
116A GLU 3.4 0.2 - - - -
117A LYS* 1.3 77.1 - - - +
119A THR* 1.3 60.9 + - + +
121A ILE* 3.6 3.3 + - - +
122A MET* 3.1 27.9 + - - +
133A VAL* 4.5 11.2 - - + -
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Residues in contact with THR 119 (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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115A ARG 3.3 7.7 + - - +
116A GLU* 2.9 20.1 + - - -
118A MET* 1.3 74.3 - - - +
120A GLN* 1.3 61.1 + - - +
122A MET* 3.2 0.9 + - - -
123A PHE* 2.8 45.6 + - - -
131A MET* 3.7 28.7 - - + -
133A VAL* 4.2 14.1 - - + -
356A ILE* 4.7 7.6 - - + -
361A TYR* 4.4 6.5 - - - -
366A PRO 4.2 2.9 + - - -
369A VAL* 3.3 35.3 - - + +
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Residues in contact with GLN 120 (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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116A GLU 3.1 10.1 + - - +
117A LYS* 3.1 43.0 + - - +
119A THR* 1.3 82.4 + - - +
121A ILE* 1.3 60.8 + - - +
123A PHE 3.7 0.2 + - - -
124A GLU* 3.1 43.9 + - - +
361A TYR* 3.3 26.4 + - + +
366A PRO* 4.8 12.5 - - + +
197G VAL* 4.6 8.5 - - - +
198G ASP 5.4 0.6 + - - +
201G SER* 4.2 13.2 + - - -
202G LYS* 4.2 17.8 - - - +
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Residues in contact with ILE 121 (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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78A TRP* 3.3 49.6 - - + +
82A GLU* 4.7 9.4 - - + -
85A TRP* 3.6 28.9 - - + -
117A LYS* 2.8 38.6 + - - +
118A MET 4.0 3.8 - - - +
120A GLN* 1.3 73.6 - - - +
122A MET* 1.3 62.7 + - - +
125A THR* 2.8 59.4 + - + +
126A PHE* 3.6 2.3 + - + -
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Residues in contact with MET 122 (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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9A ILE* 5.1 0.4 - - + -
85A TRP* 3.3 56.8 - - + +
89A PHE* 4.5 13.9 - - + -
102A VAL* 4.0 23.8 - - + -
104A LEU* 3.7 14.8 - - + -
118A MET 3.1 16.6 + - - +
119A THR 3.6 0.9 - - - +
121A ILE* 1.3 78.7 - - - +
123A PHE* 1.3 51.5 + - - +
126A PHE* 2.4 45.5 + - + +
128A THR* 3.8 9.3 - - + +
131A MET* 3.2 35.0 - - + -
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Residues in contact with PHE 123 (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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119A THR* 2.8 38.0 + - - +
122A MET* 1.3 72.5 - - - +
124A GLU* 1.3 62.2 + - - +
126A PHE 3.4 10.0 - - - +
127A ASN* 4.2 5.0 - - - +
128A THR* 4.3 11.9 - - + -
130A ALA* 4.7 2.2 - - - -
131A MET* 3.2 35.9 - - + -
356A ILE* 3.6 29.4 - - + -
357A SER 3.5 2.7 - - - -
358A LYS* 2.8 75.5 + - + +
361A TYR* 3.5 39.7 - + + -
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Residues in contact with GLU 124 (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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120A GLN* 3.1 34.3 + - - +
121A ILE* 5.2 0.2 - - - -
123A PHE* 1.3 79.0 - - - +
125A THR* 1.3 67.8 + - - +
126A PHE* 4.6 1.2 - - - -
127A ASN* 5.0 0.7 + - - +
358A LYS* 4.6 5.2 - - - +
361A TYR* 3.9 26.5 + - + +
197G VAL* 4.1 23.9 - - - +
202G LYS* 5.3 6.6 + - - -
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Residues in contact with THR 125 (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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82A GLU* 3.5 26.7 - - + +
121A ILE* 2.8 40.6 + - - +
124A GLU* 1.3 75.9 - - - +
126A PHE* 1.3 79.8 + - + +
127A ASN 4.3 0.3 + - - -
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Residues in contact with PHE 126 (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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82A GLU* 3.8 14.4 - - + -
85A TRP* 4.0 24.2 - + + -
86A HIS* 3.6 44.4 - + + -
89A PHE* 4.7 6.3 - + + -
90A TYR* 4.2 18.2 - + - -
97A PRO* 3.9 29.6 - - + -
98A GLU* 5.1 0.4 - - - -
121A ILE* 3.6 8.9 + - + -
122A MET* 2.4 45.2 - - + +
123A PHE 3.4 4.8 - - - +
124A GLU 4.6 0.7 - - - -
125A THR* 1.3 104.7 - - + +
127A ASN* 1.3 63.5 + - - +
128A THR* 3.3 2.4 + - + +
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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