Contacts of the helix formed by residues 127 - 141 (chain A) in PDB entry 1I7K
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 ASP 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ARG* 5.3 0.2 - - - +
38A GLU* 3.4 29.3 - - + +
41A THR* 3.9 19.2 - - - +
125A LEU 3.7 3.4 + - - +
126A TYR* 1.3 76.3 - - - +
128A VAL* 1.3 63.9 + - - +
129A ARG* 3.8 18.3 + - - +
130A THR* 2.7 46.2 + - - -
131A ILE* 3.2 17.6 + - - +
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Residues in contact with VAL 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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35A LEU* 4.7 0.9 - - + -
38A GLU* 2.9 29.0 + - + +
42A LEU* 4.3 6.7 - - + -
52A ALA* 4.6 0.7 - - + -
62A TRP* 3.9 41.1 - - + -
83A LEU* 4.5 12.1 - - + -
85A PHE* 3.7 29.2 - - + -
127A ASP* 1.3 72.4 - - - +
129A ARG* 1.3 63.0 + - - +
131A ILE* 3.2 10.5 + - + +
132A LEU* 3.0 42.3 + - + +
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Residues in contact with ARG 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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38A GLU 5.6 1.2 + - - +
41A THR* 4.6 10.1 - - + -
42A LEU* 3.9 28.7 - - + +
45A SER* 3.6 24.6 - - - -
47A ASP* 2.5 44.5 + - - +
50A ILE* 5.5 0.6 - - + +
127A ASP* 3.2 16.0 + - - +
128A VAL* 1.3 78.7 - - - +
130A THR* 1.3 62.9 + - - +
132A LEU* 3.3 2.9 + - - +
133A LEU* 2.9 48.9 + - + +
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Residues in contact with THR 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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117A ILE* 5.0 6.7 - - + -
126A TYR* 3.9 32.6 - - + -
127A ASP* 2.7 37.9 + - - -
129A ARG* 1.3 80.5 + - - +
131A ILE* 1.3 57.6 + - - +
133A LEU* 3.8 7.8 - - - +
134A SER* 2.9 29.2 + - - -
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Residues in contact with ILE 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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83A LEU* 4.4 13.9 - - + -
85A PHE* 5.3 4.7 - - + -
94A PRO* 3.8 20.4 - - + -
96A VAL* 4.3 9.2 - - + -
117A ILE* 4.4 8.3 - - + -
118A LEU* 4.2 17.9 - - + -
122A TRP* 3.7 33.9 - - + -
126A TYR* 4.9 2.7 - - + -
127A ASP 3.2 16.0 + - - +
128A VAL* 3.2 14.1 + - + +
130A THR* 1.3 72.9 - - - +
132A LEU* 1.3 68.4 + - + +
134A SER* 3.3 6.6 + - - -
135A ILE* 3.0 42.0 + - + +
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Residues in contact with LEU 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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42A LEU* 4.1 8.3 - - + -
50A ILE* 3.2 38.6 - - + -
51A SER 4.3 4.5 - - - +
52A ALA* 3.8 26.5 - - + -
64A GLY* 5.4 2.9 - - - -
66A ILE* 3.4 24.5 - - + +
81A LEU* 5.6 4.9 - - + -
83A LEU* 4.5 27.6 - - + -
96A VAL* 6.0 0.2 - - + -
128A VAL* 3.0 28.8 + - + +
129A ARG 3.8 2.9 - - - +
131A ILE* 1.3 79.2 - - + +
133A LEU* 1.3 57.2 + - - +
135A ILE* 3.3 5.8 + - + -
136A GLN* 2.9 26.9 + - - +
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Residues in contact with LEU 133 (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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47A ASP* 4.3 21.1 - - + +
48A LYS 5.7 0.7 - - - +
50A ILE* 4.5 7.4 - - + -
129A ARG* 2.9 62.5 + - + +
130A THR* 3.8 6.7 - - - +
132A LEU* 1.3 76.6 - - - +
134A SER* 1.3 57.9 + - - +
136A GLN* 3.3 22.6 + - - +
137A SER* 2.9 30.5 + - - -
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Residues in contact with SER 134 (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 LEU* 3.6 17.3 - - - +
117A ILE* 3.5 29.2 - - - +
130A THR* 2.9 20.5 + - - -
131A ILE 3.6 4.7 - - - -
132A LEU 3.2 0.2 - - - -
133A LEU* 1.3 77.6 - - - +
135A ILE* 1.3 56.2 + - - +
137A SER* 3.3 7.9 + - - -
138A LEU* 3.0 27.2 + - - +
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Residues in contact with ILE 135 (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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66A ILE* 3.8 16.2 - - + -
81A LEU* 4.2 8.7 - - + -
96A VAL* 3.6 31.6 - - + -
98A PHE* 3.9 29.2 - - + -
113A ILE* 4.2 8.7 - - + -
115A LEU* 3.7 19.7 - - + -
118A LEU* 4.6 2.7 - - + -
131A ILE* 3.0 29.0 + - + +
132A LEU* 3.8 7.9 - - + +
134A SER* 1.3 72.2 - - - +
136A GLN* 1.3 68.2 + - - +
138A LEU* 3.1 19.8 + - + +
139A LEU* 3.2 14.1 + - + +
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Residues in contact with GLN 136 (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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48A LYS* 3.5 23.1 + - - +
49A GLY* 3.8 3.8 + - - -
50A ILE* 3.6 21.2 - - + +
66A ILE* 3.9 16.7 - - + +
67A HIS* 2.9 28.2 + - - +
68A GLY* 4.6 1.1 - - - -
69A ALA* 4.3 28.1 + - + +
132A LEU 2.9 17.9 + - - +
133A LEU* 3.3 18.1 + - - +
135A ILE* 1.3 75.4 - - - +
137A SER* 1.3 63.1 + - - +
139A LEU* 3.4 19.7 - - - +
140A GLY 3.9 1.9 + - - -
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Residues in contact with SER 137 (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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69A ALA* 6.2 1.8 - - - -
133A LEU 2.9 17.3 + - - -
134A SER* 3.5 8.5 - - - -
136A GLN* 1.3 78.4 - - - +
138A LEU* 1.3 61.4 + - - +
140A GLY* 3.2 4.9 + - - -
141A GLU* 3.1 27.8 + - - +
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Residues in contact with LEU 138 (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 PHE* 6.3 0.7 - - + -
104A HIS* 3.0 21.1 + - + -
106A ASN* 3.6 26.5 - - + +
107A VAL* 5.7 2.2 - - + -
113A ILE* 3.7 29.2 - - + -
114A SER 4.1 12.6 - - - +
115A LEU* 4.2 23.8 - - + -
134A SER 3.0 13.7 + - - +
135A ILE* 3.1 13.7 + - + +
137A SER* 1.3 73.7 - - - +
139A LEU* 1.3 68.0 + - + +
141A GLU 3.2 28.3 + - - +
142A PRO* 4.2 0.7 - - + -
143A ASN* 4.4 5.8 - - + +
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Residues in contact with LEU 139 (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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66A ILE* 4.1 25.8 - - + -
68A GLY* 4.2 19.7 - - - -
69A ALA 5.7 0.4 - - - +
72A THR* 5.8 0.2 - - - +
74A TYR* 3.0 48.4 - - + -
79A TYR* 4.4 15.5 - - + -
98A PHE* 4.4 14.4 - - + -
102A CYS* 4.2 17.9 - - - -
104A HIS* 3.3 25.2 + - + -
135A ILE* 3.2 11.1 + - + +
136A GLN 3.4 10.3 - - - +
137A SER 3.2 0.2 - - - -
138A LEU* 1.3 80.7 - - + +
140A GLY* 1.3 59.4 + - - +
142A PRO* 4.0 4.3 - - - +
156A TRP* 4.2 1.2 - - - -
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Residues in contact with GLY 140 (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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69A ALA* 6.4 0.2 - - - +
72A THR* 4.2 30.7 - - - +
74A TYR* 4.4 1.1 - - - -
136A GLN 3.9 2.4 + - - -
137A SER 3.2 6.8 + - - -
138A LEU 3.2 0.2 - - - -
139A LEU* 1.3 79.1 - - - +
141A GLU* 1.3 62.5 + - - +
142A PRO* 3.5 6.5 - - - +
156A TRP* 3.8 14.9 - - - -
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Residues in contact with GLU 141 (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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137A SER* 3.1 19.7 + - - +
138A LEU* 3.2 16.6 + - - +
140A GLY* 1.3 81.1 - - - +
142A PRO* 1.3 70.0 - - - +
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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