Contacts of the helix formed by residues 97 - 113 (chain A) in PDB entry 1CXQ
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 THR 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A PHE* 4.2 1.4 - - - -
95A ARG* 3.3 23.8 + - + -
96A VAL* 1.3 80.7 - - - +
98A SER* 1.3 64.6 + - - +
99A VAL* 3.5 8.0 + - - +
100A ALA* 2.9 25.2 + - - +
101A ALA* 3.1 16.3 + - - +
125A CYS* 3.5 15.1 - - - +
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Residues in contact with SER 98 (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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97A THR* 1.3 74.2 - - - +
99A VAL* 1.3 65.7 + - - +
101A ALA* 3.2 4.9 + - - +
102A GLN* 3.0 33.7 + - - +
124A SER 3.8 0.5 + - - -
125A CYS* 3.5 22.2 + - - +
128A SER* 2.7 29.5 + - - -
130A SER* 4.2 8.7 - - - -
131A THR* 3.4 11.6 + - - -
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Residues in contact with VAL 99 (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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97A THR* 3.3 6.2 + - - +
98A SER* 1.3 78.5 - - - +
100A ALA* 1.3 57.9 + - - +
102A GLN* 3.2 20.5 + - + +
103A HIS* 2.8 60.0 + - + +
130A SER* 4.9 5.4 - - - +
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Residues in contact with ALA 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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65A PHE* 4.1 8.5 - - + -
93A HIS* 3.5 30.3 - - + +
95A ARG 3.6 18.6 - - - +
97A THR* 2.9 24.2 + - - +
99A VAL* 1.3 76.6 - - - +
101A ALA* 1.4 61.9 + - - +
103A HIS* 3.3 6.5 + - - -
104A HIS* 2.9 24.3 + - - +
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Residues in contact with ALA 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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63A THR* 6.1 0.4 - - + -
65A PHE* 3.7 21.6 - - + -
97A THR 3.1 12.0 + - - +
98A SER 3.4 8.5 - - - +
100A ALA* 1.4 76.1 - - - +
102A GLN* 1.3 58.6 + - - +
104A HIS* 3.3 7.6 + - - +
105A TRP* 2.9 44.0 + - + -
125A CYS 4.2 10.8 - - - +
126A PHE* 4.0 18.8 - - + -
131A THR* 4.9 0.2 - - - +
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Residues in contact with GLN 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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98A SER 3.0 16.9 + - - +
99A VAL* 3.2 15.9 + - - +
101A ALA* 1.3 73.9 - - - +
103A HIS* 1.3 69.2 + - + +
105A TRP* 3.3 6.6 + - + -
106A ALA* 2.9 21.2 + - - +
130A SER* 2.9 28.0 + - - +
131A THR* 3.1 31.1 + - - +
134A TRP* 3.4 60.6 - - + +
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Residues in contact with HIS 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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91A THR* 5.6 0.2 - - - +
93A HIS* 4.5 10.1 - - + -
99A VAL* 2.8 46.8 + - + +
100A ALA* 3.7 8.1 - - - +
102A GLN* 1.3 74.9 - - - +
104A HIS* 1.3 63.1 + - - +
106A ALA* 3.3 7.9 + - - +
107A THR* 3.2 24.3 + - - -
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Residues in contact with HIS 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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63A THR* 4.0 8.5 - - + -
78A ALA* 3.2 38.5 - - + +
79A VAL 3.9 2.0 - - - -
80A THR* 2.6 32.1 + - - -
89A VAL* 3.4 27.6 - - + -
91A THR* 2.9 35.9 + - - +
93A HIS* 3.9 1.7 - - - +
100A ALA 2.9 13.9 + - - +
101A ALA* 3.4 9.4 - - - +
103A HIS* 1.3 76.5 - - - +
105A TRP* 1.3 71.6 + + - +
107A THR* 3.1 6.4 + - - +
108A ALA* 2.9 24.4 + - - +
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Residues in contact with TRP 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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61A TRP* 3.9 17.0 - + + -
63A THR* 2.9 27.6 + - + +
80A THR* 3.9 4.5 - - - -
101A ALA* 2.9 29.4 + - + +
102A GLN* 3.3 2.2 + - + +
104A HIS* 1.3 85.9 - + - +
106A ALA* 1.3 67.1 + - - +
108A ALA* 3.7 2.9 - - + +
109A ILE* 2.8 30.5 + - + +
118A ILE* 3.7 22.6 - - + +
120A THR* 3.8 24.7 - - + -
126A PHE* 3.7 28.5 - + - -
131A THR* 3.6 28.0 - - + -
134A TRP* 3.5 33.9 - + + -
135A LEU* 3.9 19.5 - - + -
142A HIS* 5.1 0.9 - - - -
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Residues in contact with ALA 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 GLN 2.9 17.3 + - - +
103A HIS* 3.5 9.0 - - - +
104A HIS 3.2 0.2 - - - -
105A TRP* 1.3 76.7 - - - +
107A THR* 1.3 63.0 + - - +
109A ILE* 3.4 6.3 + - - +
110A ALA* 3.2 20.8 + - - +
134A TRP* 3.8 15.6 - - + +
138A TRP* 5.5 6.0 - - + -
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Residues in contact with THR 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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89A VAL* 4.4 5.2 - - + -
91A THR* 4.0 23.8 - - + +
103A HIS 3.2 9.9 + - - -
104A HIS 3.1 8.8 + - - -
106A ALA* 1.3 76.8 - - - +
108A ALA* 1.3 65.9 + - - +
110A ALA* 3.1 9.3 + - + +
111A VAL* 3.1 23.6 + - + +
301A GOL 3.8 25.6 - - - +
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Residues in contact with ALA 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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61A TRP* 3.6 25.6 - - + -
80A THR* 4.5 4.5 - - + +
89A VAL* 4.0 29.8 - - + +
104A HIS* 2.9 24.0 + - - +
105A TRP* 3.1 4.9 + - - +
107A THR* 1.3 75.6 - - - +
109A ILE* 1.3 58.0 + - - +
111A VAL* 3.2 0.9 + - - -
112A LEU* 2.8 35.4 + - + +
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Residues in contact with ILE 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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61A TRP* 3.8 15.3 - - + -
105A TRP* 2.8 25.1 + - + +
106A ALA* 3.7 4.9 - - - +
108A ALA* 1.3 69.0 - - - +
110A ALA* 1.3 63.2 + - - +
113A GLY* 2.8 43.3 + - - +
114A ARG* 4.2 4.9 - - + +
115A PRO* 4.2 6.1 - - + -
134A TRP* 3.9 14.8 - - + -
138A TRP* 3.8 55.4 - - + -
140A ILE* 3.9 13.9 - - + -
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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 ALA 3.2 12.4 + - - +
107A THR* 3.1 13.5 + - + +
109A ILE* 1.3 78.7 - - - +
111A VAL* 1.3 64.2 + - + +
113A GLY 4.8 0.3 + - - -
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Residues in contact with VAL 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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89A VAL* 3.9 26.2 - - + -
107A THR* 3.1 17.3 + - + +
108A ALA 3.7 5.4 - - - +
110A ALA* 1.3 81.7 - - + +
112A LEU* 1.3 69.5 + - + +
113A GLY 3.6 0.2 - - - -
193A MET* 4.5 11.9 - - + -
197A ASN* 6.0 1.3 - - - +
301A GOL 4.4 17.0 - - - +
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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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61A TRP* 3.7 36.3 + - + +
80A THR* 4.2 11.7 - - + -
82A ASP* 4.2 19.7 - - + +
85A SER* 5.1 0.4 - - - +
87A ALA* 4.0 28.7 - - + +
88A ILE 5.7 0.2 - - - +
89A VAL* 3.7 24.7 - - + +
108A ALA* 2.8 16.5 + - + +
111A VAL* 1.3 85.5 - - + +
113A GLY* 1.3 56.4 + - - +
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Residues in contact with GLY 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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61A TRP* 3.2 25.5 - - - -
109A ILE* 2.8 25.2 + - - -
110A ALA 4.7 0.4 + - - -
111A VAL 3.6 1.0 - - - -
112A LEU* 1.3 80.0 - - - +
114A ARG* 1.3 60.5 + - - -
115A PRO* 3.5 0.3 - - - +
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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