Contacts of the helix formed by residues 1126 - 1139 (chain A) in PDB entry 5UAK
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 GLU1126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 5.1 13.0 - - + +
109A TYR* 3.7 26.2 - - - +
110A ASP* 4.2 10.3 - - - +
111A PRO* 6.3 2.9 - - - -
333A LEU* 3.7 28.6 - - + +
337A PHE* 5.4 1.8 - - - -
1124A GLU 4.8 1.6 - - - +
1125A GLY* 1.3 78.6 - - - -
1127A GLY* 1.3 67.9 + - - +
1128A ARG 3.4 0.2 - - - -
1129A VAL* 3.7 6.5 + - - +
1130A GLY* 3.6 13.2 + - - -
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Residues in contact with GLY1127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 5.5 3.1 - - - -
337A PHE* 4.6 15.3 - - - -
917A TYR* 4.8 10.7 + - - -
1125A GLY* 4.7 0.2 - - - -
1126A GLU* 1.3 80.0 - - - +
1128A ARG* 1.3 55.2 + - - +
1129A VAL 3.1 2.5 - - - -
1130A GLY 2.9 3.6 + - - -
1131A ILE* 2.8 49.5 + - - +
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Residues in contact with ARG1128 (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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881A LEU 5.1 8.3 + - - -
1011A LEU* 3.9 55.5 + - + +
1012A GLN* 5.0 18.4 + - + +
1123A GLY* 5.7 9.0 - - - -
1124A GLU* 5.8 1.9 - - - +
1125A GLY* 4.4 19.7 - - - +
1126A GLU 3.4 0.8 - - - +
1127A GLY* 1.3 74.2 - - - +
1129A VAL* 1.3 63.0 + - + +
1131A ILE* 4.4 2.4 - - - +
1132A ILE* 3.6 22.0 - - + +
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Residues in contact with VAL1129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 4.2 21.5 - - + +
106A ILE* 4.6 4.9 - - + -
109A TYR* 4.1 30.1 - - + -
1012A GLN* 6.1 1.8 - - - +
1118A SER* 5.2 18.0 - - - +
1119A ILE* 5.9 2.2 - - + -
1123A GLY* 5.1 11.0 - - - -
1125A GLY 3.9 17.0 - - - +
1126A GLU 3.7 8.2 + - - +
1127A GLY 3.1 0.4 - - - -
1128A ARG* 1.3 79.5 - - + +
1130A GLY* 1.3 64.2 + - - +
1132A ILE* 4.4 1.2 - - - +
1133A LEU* 3.2 47.4 + - + +
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Residues in contact with GLY1130 (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 ILE* 3.7 27.3 - - - +
337A PHE* 4.5 11.9 - - - -
1126A GLU 3.6 5.9 + - - -
1127A GLY 2.9 6.7 + - - -
1129A VAL* 1.3 79.2 - - - +
1131A ILE* 1.3 52.0 + - - +
1133A LEU* 3.4 1.2 + - - +
1134A THR* 2.7 45.5 + - - +
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Residues in contact with ILE1131 (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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337A PHE* 4.2 16.6 - - + -
881A LEU* 4.5 31.9 - - + -
917A TYR* 4.0 27.6 - - + +
920A VAL* 5.8 3.1 - - + +
921A GLY* 5.3 8.3 - - - -
1007A VAL* 6.5 0.2 - - + -
1008A VAL* 6.4 0.2 - - + -
1011A LEU* 5.2 3.8 - - + -
1127A GLY 2.8 30.6 + - - +
1128A ARG* 4.5 3.1 - - - +
1130A GLY* 1.3 69.9 - - - +
1132A ILE* 1.3 70.3 + - + +
1134A THR* 2.8 19.1 + - - -
1135A LEU* 2.9 40.9 + - + +
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Residues in contact with ILE1132 (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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1007A VAL 5.0 0.2 - - - +
1008A VAL* 3.8 44.4 - - + +
1011A LEU* 3.8 35.0 - - + -
1012A GLN* 4.7 13.7 - - + +
1015A ILE* 4.6 4.0 - - + -
1114A VAL* 3.8 28.0 - - + -
1118A SER* 5.1 7.2 - - - -
1128A ARG* 3.6 21.3 + - + +
1129A VAL 3.9 2.6 + - - +
1130A GLY 3.4 0.2 - - - -
1131A ILE* 1.3 86.7 - - + +
1133A LEU* 1.3 60.0 + - + +
1135A LEU* 3.8 0.7 - - - +
1136A ALA* 2.8 33.8 + - - +
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Residues in contact with LEU1133 (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 LEU* 3.8 16.6 - - + -
105A ILE* 3.5 31.2 - - + -
106A ILE* 3.8 10.3 - - + -
1111A PHE* 5.3 1.3 - - + -
1114A VAL* 5.7 1.6 - - + -
1115A THR* 3.8 30.5 - - + -
1118A SER* 4.2 17.3 - - - +
1119A ILE* 5.5 3.6 - - + -
1129A VAL* 3.2 31.6 + - + +
1130A GLY 3.8 1.8 - - - +
1131A ILE 3.3 0.4 - - - -
1132A ILE* 1.3 81.5 - - + +
1134A THR* 1.3 57.5 + - - +
1136A ALA* 4.2 3.0 - - + +
1137A MET* 3.0 47.3 + - + +
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Residues in contact with THR1134 (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 LEU* 4.0 22.2 - - + -
106A ILE* 5.7 0.2 - - + -
337A PHE* 3.9 40.8 - - + +
340A ILE* 5.7 8.6 - - + +
341A SER* 5.6 4.6 - - - +
921A GLY* 5.2 4.8 + - - -
1130A GLY* 2.7 29.3 + - - +
1131A ILE* 2.8 19.1 + - - -
1133A LEU* 1.3 73.4 - - - +
1135A LEU* 1.3 65.4 + - - +
1137A MET* 4.3 3.3 - - - +
1138A ASN* 3.7 21.0 + - - +
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Residues in contact with LEU1135 (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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920A VAL 4.6 4.7 - - - +
921A GLY* 3.3 30.1 - - - +
923A ALA* 4.7 13.2 - - + -
1004A ALA* 4.2 17.7 - - + +
1007A VAL* 3.9 28.9 - - + -
1008A VAL* 4.0 17.9 - - + -
1131A ILE* 2.9 43.4 + - + +
1132A ILE 3.9 2.5 - - - +
1134A THR* 1.3 81.4 + - - +
1136A ALA* 1.3 63.0 + - - +
1138A ASN* 4.2 0.5 - - - +
1139A ILE* 3.3 28.8 + - - +
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Residues in contact with ALA1136 (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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1008A VAL* 5.1 6.3 - - + +
1107A PHE* 3.5 25.0 - - + -
1110A PHE* 5.8 6.5 - - + -
1111A PHE* 3.5 21.3 - - + -
1114A VAL* 4.4 20.6 - - + -
1132A ILE* 2.8 23.5 + - + +
1133A LEU* 4.2 2.7 - - + +
1135A LEU* 1.3 74.3 - - - +
1137A MET* 1.3 62.1 + - - +
1139A ILE* 3.5 7.8 - - - +
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Residues in contact with MET1137 (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 GLN* 3.9 27.5 + - - +
99A PRO* 5.4 3.1 - - - -
102A LEU* 3.7 45.3 - - + -
105A ILE* 6.3 1.3 - - + -
127A LEU* 3.6 39.5 - - + -
341A SER* 5.7 6.3 - - - -
1111A PHE* 3.4 22.2 - - + -
1115A THR* 5.6 0.2 - - + -
1133A LEU* 3.0 31.8 + - + +
1134A THR* 4.3 4.0 - - - +
1135A LEU 3.3 0.2 - - - -
1136A ALA* 1.3 77.3 - - - +
1138A ASN* 1.3 63.2 + - + +
1139A ILE 3.5 0.9 + - - -
1140A MET* 3.2 28.3 - - - +
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Residues in contact with ASN1138 (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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340A ILE* 4.3 2.9 + - + +
341A SER* 3.8 27.9 + - - +
344A ILE* 3.2 45.2 - - - +
345A VAL* 4.9 6.1 - - - +
348A MET* 5.7 0.5 - - - +
1134A THR 3.7 12.0 + - - +
1135A LEU 3.7 3.1 + - - +
1137A MET* 1.3 77.5 - - + +
1139A ILE* 1.3 61.6 + - - +
1140A MET* 3.5 2.5 - - - -
1141A SER* 3.4 18.2 + - - -
1142A THR* 5.3 1.7 - - - +
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Residues in contact with ILE1139 (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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1000A ILE* 5.5 2.0 - - + +
1001A VAL* 4.2 29.8 - - + +
1004A ALA* 3.9 28.0 - - + -
1005A ILE* 4.8 5.4 - - + +
1107A PHE* 3.5 31.0 - - + -
1135A LEU 3.3 14.9 + - - +
1136A ALA* 3.5 12.1 - - - +
1137A MET 3.4 0.2 - - - -
1138A ASN* 1.3 74.7 - - - +
1140A MET* 1.3 58.1 + - - +
1141A SER 3.2 3.1 - - - -
1142A THR* 2.6 51.2 + - - +
1143A LEU* 3.3 4.5 + - + -
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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