Contacts of the helix formed by residues 117 - 132 (chain A) in PDB entry 6Q6Q
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 CYS 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 5.0 11.9 - - + +
111A GLY 5.8 1.1 - - - -
116A PHE* 1.3 78.2 - - - +
118A THR* 1.3 67.2 + - - +
119A PRO* 3.4 0.7 - - - -
120A GLY* 3.2 5.9 + - - -
121A MET* 3.1 29.5 + - + +
147A ASN* 5.9 0.2 - - - +
148A LEU 3.4 19.7 - - - +
149A CYS* 3.1 16.8 - - - -
157A ILE* 5.3 2.2 - - - -
753A MET* 4.4 8.7 - - + +
3001A FES 2.2 47.1 - - - -
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 4.4 7.9 - - + -
111A GLY 4.4 2.9 + - - -
112A THR* 3.3 34.2 - - + +
115A GLY* 3.4 19.4 - - - -
116A PHE 3.2 0.4 - - - -
117A CYS* 1.3 80.8 - - - +
119A PRO* 1.3 70.4 - - - +
121A MET* 3.0 9.4 + - - +
122A VAL* 2.8 30.0 + - + +
592A HIS 3.3 17.5 - - - +
593A ALA* 3.6 16.8 - - + -
3001A FES 4.9 0.2 - - - -
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Residues in contact with PRO 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLY 3.3 27.6 - - - +
40A THR* 5.0 0.9 - - - -
41A LYS* 3.9 15.0 - - + +
51A ALA 4.7 3.8 - - - +
53A THR 5.1 0.9 - - - -
89A VAL* 3.5 26.2 - - + +
115A GLY 3.4 10.5 - - - +
116A PHE 3.3 15.9 - - - +
117A CYS 3.6 0.4 - - - -
118A THR* 1.3 89.6 - - - +
120A GLY* 1.3 59.7 + - - +
122A VAL* 3.6 1.6 + - + +
123A MET* 3.3 29.5 + - - +
592A HIS 3.7 11.2 - - - +
595A GLY* 4.5 5.6 - - - -
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Residues in contact with GLY 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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50A GLY 3.3 24.7 - - - -
51A ALA 4.0 10.6 + - - -
53A THR* 3.7 12.0 - - - -
117A CYS 3.2 8.3 + - - -
119A PRO* 1.3 76.0 - - - +
121A MET* 1.3 63.9 + - - +
123A MET 3.6 0.3 + - - -
124A SER* 3.1 27.7 + - - -
147A ASN* 3.7 4.4 + - - -
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 3.6 19.7 - - + -
117A CYS* 3.1 18.3 + - + +
118A THR* 3.0 9.5 + - - +
120A GLY* 1.3 77.3 - - - +
122A VAL* 1.3 62.4 + - - +
124A SER* 3.4 2.1 + - - -
125A ILE* 3.1 30.6 + - - +
144A LEU* 4.0 15.0 - - + -
147A ASN* 3.5 38.6 - - + +
148A LEU 3.7 23.6 - - - +
149A CYS* 3.8 19.1 - - + -
154A TYR* 4.1 8.3 - - + -
157A ILE* 3.8 25.8 - - + -
1241A ILE* 6.2 0.2 - - - -
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.5 4.7 - - + -
92A ILE* 3.6 28.3 - - + -
102A VAL* 3.6 17.2 - - + +
103A GLN* 3.7 13.7 - - + -
106A ILE* 3.8 30.3 - - + -
118A THR* 2.8 25.3 + - + +
119A PRO* 4.0 5.6 - - + +
120A GLY 3.3 0.2 - - - -
121A MET* 1.3 75.0 - - - +
123A MET* 1.3 58.7 + - - +
125A ILE 3.4 0.7 + - - -
126A TYR* 2.8 27.5 + - - +
593A ALA* 3.7 19.5 - - + +
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Residues in contact with MET 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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53A THR* 3.2 34.8 - - + +
54A VAL* 4.5 0.4 - - - -
55A MET* 3.8 24.9 - - + +
87A THR* 3.2 28.9 - - + +
88A THR* 3.5 23.6 - - - +
89A VAL* 3.8 17.5 - - + +
92A ILE* 4.2 14.4 - - - -
119A PRO 3.3 14.3 + - - +
120A GLY 3.6 0.2 + - - -
121A MET 3.3 0.2 - - - -
122A VAL* 1.3 74.4 - - - +
124A SER* 1.3 58.2 + - - +
126A TYR* 3.8 11.8 - - + +
127A THR* 2.6 39.4 + - - +
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Residues in contact with SER 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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53A THR* 3.3 16.7 - - - +
70A PRO* 5.3 5.2 - - - +
120A GLY 3.1 9.3 + - - -
121A MET 3.8 2.2 - - - -
123A MET* 1.3 79.4 - - - +
125A ILE* 1.3 61.4 + - - +
127A THR* 4.0 3.9 - - - -
128A LEU* 3.2 23.7 + - - +
143A ALA* 4.1 19.9 - - - +
144A LEU* 4.2 4.7 - - - -
147A ASN* 2.8 35.7 + - - -
348A GLN* 3.6 6.5 + - - -
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Residues in contact with ILE 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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102A VAL* 3.8 18.2 - - + -
106A ILE* 4.0 25.4 - - + -
121A MET 3.1 18.6 + - - +
124A SER* 1.3 72.4 - - - +
126A TYR* 1.3 66.7 + - - +
128A LEU* 3.5 1.7 + - - +
129A LEU* 3.1 41.2 + - + +
140A LEU* 3.8 20.6 - - + +
143A ALA* 5.8 0.2 - - - -
144A LEU* 3.8 19.3 - - + -
157A ILE* 4.3 4.0 - - + +
160A ALA* 5.9 2.0 - - + -
161A CYS* 3.7 24.7 - - - +
164A PHE* 4.5 10.3 - - + -
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Residues in contact with TYR 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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55A MET* 3.6 26.2 - - + -
87A THR* 4.5 0.9 - - + -
92A ILE* 3.7 36.1 - - + -
100A HIS* 3.2 44.9 - + - -
102A VAL* 4.2 9.8 - - + +
122A VAL 2.8 19.1 + - - +
123A MET* 3.8 17.0 - - + +
125A ILE* 1.3 77.9 - - - +
127A THR* 1.3 63.0 + - - +
129A LEU* 3.3 5.6 + - + +
130A ARG* 3.0 54.8 + - + +
215A GLU* 4.0 10.6 - - - +
216A LEU* 3.8 22.2 + - - +
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Residues in contact with THR 127 (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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54A VAL 4.8 0.3 + - - -
55A MET* 3.6 42.9 + - + +
68A HIS* 4.5 1.1 - - + -
69A HIS* 3.9 7.0 - - - +
70A PRO* 3.6 43.7 - - + +
123A MET* 2.6 24.8 + - - +
124A SER 4.0 2.9 - - - -
126A TYR* 1.3 76.5 - - - +
128A LEU* 1.3 62.9 + - - +
130A ARG* 3.2 11.8 + - - +
131A ASN* 3.3 18.6 + - - +
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Residues in contact with LEU 128 (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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124A SER 3.2 16.3 + - - +
125A ILE 3.9 3.1 - - - +
126A TYR 3.3 0.2 - - - -
127A THR* 1.3 78.9 - - - +
129A LEU* 1.3 52.9 + - - +
131A ASN* 3.0 9.7 + - + +
132A HIS* 2.7 49.8 + - + +
135A PRO* 4.5 9.6 - - + -
139A GLN* 3.4 45.3 - - + +
140A LEU* 3.6 25.4 - - + +
143A ALA* 4.0 13.9 - - + -
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Residues in contact with LEU 129 (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 HIS* 6.1 0.2 - - + -
102A VAL* 3.6 24.0 - - + -
125A ILE* 3.1 32.9 + - + +
126A TYR* 3.3 6.7 + - + +
128A LEU* 1.3 76.1 - - - +
130A ARG* 1.3 61.7 + - - +
131A ASN 3.3 0.2 - - - -
132A HIS 3.7 7.0 - - - +
133A PRO* 3.5 25.1 - - - +
135A PRO* 3.7 31.0 - - + -
140A LEU* 5.0 4.7 - - + -
164A PHE* 3.6 40.6 - - + -
210A LEU* 4.0 22.0 - - + +
215A GLU* 5.2 3.1 - - - +
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Residues in contact with ARG 130 (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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55A MET* 4.5 11.9 - - - +
68A HIS* 3.1 46.1 + - + -
126A TYR* 3.0 54.8 + - + +
127A THR* 3.5 11.0 - - - +
128A LEU 3.1 0.6 - - - -
129A LEU* 1.3 76.8 - - - +
131A ASN* 1.3 63.1 + - - +
133A PRO* 5.0 5.1 - - - +
215A GLU* 3.6 37.9 - - - +
216A LEU* 3.4 29.2 + - - +
218A PHE 5.8 0.6 - - - +
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Residues in contact with ASN 131 (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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68A HIS* 3.2 41.9 + - - +
69A HIS* 4.9 1.4 - - - +
70A PRO* 5.3 2.4 - - - +
127A THR* 3.3 18.5 + - - +
128A LEU* 3.0 10.8 + - + +
130A ARG* 1.3 83.2 - - - +
132A HIS* 1.3 82.6 + - + +
133A PRO* 3.9 5.5 - - - +
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Residues in contact with HIS 132 (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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128A LEU* 2.7 28.5 + - + +
129A LEU* 3.7 11.6 - - - -
131A ASN* 1.3 96.0 + - + +
133A PRO* 1.3 69.6 - - - +
134A GLU 3.1 5.1 + - - +
135A PRO* 3.4 22.7 - - + +
139A GLN* 3.8 38.8 + - - +
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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