Contacts of the helix formed by residues 1118 - 1130 (chain A) in PDB entry 1F38
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 ALA1118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1104A ASP* 3.6 10.3 - - - +
1116A PRO 3.4 2.4 + - - -
1117A THR* 1.3 77.0 - - - +
1119A MSE 1.3 67.1 + - - +
1120A GLU* 3.8 6.7 - - - +
1121A VAL* 2.9 20.2 + - + +
1122A ARG* 2.9 18.9 + - - +
1261A ILE* 4.2 9.2 - - + -
1263A ARG* 3.6 15.7 - - - +
1276A ARG* 4.8 11.9 - - + -
1279A VAL* 5.8 3.5 - - + +
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Residues in contact with MSE1119 (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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1101A MSE 3.6 39.3 - - + +
1102A ILE 3.6 13.0 - - - +
1103A PRO* 4.0 19.7 - - + -
1104A ASP* 2.9 14.8 + - - +
1118A ALA* 1.3 72.2 - - - +
1120A GLU* 1.3 62.7 + - - +
1122A ARG* 3.2 25.0 + - - +
1123A CYS* 2.7 36.0 + - - +
1263A ARG* 3.8 1.9 - - - +
4124D LEU* 4.6 16.6 - - - -
4127D CYS* 4.7 9.6 - - + +
4128D LEU* 5.1 13.7 - - + -
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Residues in contact with GLU1120 (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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1118A ALA* 3.8 3.8 - - - +
1119A MSE 1.3 79.0 + - - +
1121A VAL* 1.3 60.8 + - - +
1123A CYS* 3.5 8.3 - - - +
1124A LEU* 3.3 19.8 + - - +
1259A LEU* 4.2 6.3 - - + +
1261A ILE* 3.5 32.7 - - + +
1263A ARG* 2.9 41.3 + - - -
4124D LEU* 3.8 35.8 - - + +
4257D THR* 3.9 17.8 + - + +
4259D LEU* 4.7 4.0 - - + -
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Residues in contact with VAL1121 (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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1117A THR* 3.6 21.8 - - + -
1118A ALA* 2.9 15.3 + - + +
1120A GLU* 1.3 76.8 - - - +
1122A ARG* 1.3 66.4 + - - +
1124A LEU* 3.0 4.4 + - - +
1125A ILE* 2.9 26.1 + - + +
1233A THR* 5.2 0.4 - - - +
1259A LEU* 4.2 15.3 - - + -
1261A ILE* 4.1 19.7 - - + -
1279A VAL* 4.0 29.6 - - + -
1281A LEU* 4.1 27.4 - - + -
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Residues in contact with ARG1122 (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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1101A MSE 3.6 17.0 - - - +
1102A ILE 2.8 30.5 + - - -
1104A ASP* 2.9 32.1 + - - +
1107A PHE* 3.7 16.4 - - - -
1116A PRO* 4.7 0.6 - - - +
1117A THR* 3.0 32.6 + - + +
1118A ALA 2.9 9.8 + - - +
1119A MSE 3.3 15.7 - - - +
1121A VAL* 1.3 75.5 - - - +
1123A CYS* 1.3 66.6 + - - +
1125A ILE* 3.0 20.4 + - - +
1126A MSE 3.1 15.9 + - - +
1146A GLY* 3.7 31.8 - - - -
1147A VAL* 4.5 9.6 - - + -
1150A GLU* 3.0 26.7 + - + -
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Residues in contact with CYS1123 (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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1101A MSE 4.0 8.4 - - - -
1119A MSE 2.7 21.7 + - - +
1120A GLU* 3.5 11.4 - - - +
1122A ARG* 1.3 73.2 - - - +
1124A LEU* 1.3 62.7 + - - +
1126A MSE 3.2 11.1 + - - +
1127A CYS 3.3 8.1 + - - -
4123D CYS* 3.5 32.6 - - - -
4124D LEU* 3.9 7.2 - - + -
4127D CYS* 2.1 52.3 - - + -
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Residues in contact with LEU1124 (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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1120A GLU 3.3 8.8 + - - +
1121A VAL* 3.0 9.8 + - - +
1123A CYS* 1.3 78.9 - - - +
1125A ILE* 1.3 65.4 + - - +
1127A CYS* 3.0 25.3 + - + +
1128A LEU* 3.0 25.5 + - + +
1257A THR* 4.4 9.4 - - + -
1259A LEU* 4.0 19.5 - - + -
1281A LEU* 3.7 23.3 - - + -
4119D MSE 4.5 9.6 - - - -
4120D GLU* 3.8 43.7 - - + +
4123D CYS* 3.8 9.4 - - + -
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Residues in contact with ILE1125 (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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1117A THR* 4.8 3.6 - - + -
1121A VAL* 2.9 29.9 + - + +
1122A ARG* 3.4 11.0 - - - +
1124A LEU* 1.3 76.9 - - - +
1126A MSE 1.3 64.4 + - - +
1128A LEU* 3.5 4.2 + - - -
1129A ALA* 2.8 26.8 + - + +
1147A VAL* 3.9 31.2 - - + -
1205A VAL* 4.1 30.5 - - + -
1231A ILE* 3.7 12.2 - - + +
1233A THR* 3.9 20.2 - - - +
1281A LEU* 4.2 19.3 - - + -
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Residues in contact with MSE1126 (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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1101A MSE 4.5 3.8 - - + -
1122A ARG 3.1 14.1 + - - +
1123A CYS* 3.5 7.4 - - - +
1124A LEU 3.0 0.6 - - - -
1125A ILE* 1.3 84.1 - - - +
1127A CYS* 1.3 66.1 + - - +
1129A ALA* 4.2 2.9 - - - -
1130A GLU* 2.9 20.8 + - - -
1131A PRO* 3.2 41.1 - - + +
1147A VAL* 4.8 2.7 - - - +
1150A GLU* 3.5 33.7 - - + +
1151A LEU* 3.9 24.0 - - + -
1154A ARG* 3.4 52.0 - - - +
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Residues in contact with CYS1127 (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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1123A CYS 3.3 3.0 + - - -
1124A LEU* 3.0 15.2 + - + +
1126A MSE 1.3 79.2 - - - +
1128A LEU* 1.3 63.9 + - + +
1130A GLU* 3.4 18.5 - - - +
4101D MSE 3.5 47.7 + - + +
4119D MSE 4.7 7.7 - - - +
4123D CYS* 2.1 49.1 - - - -
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Residues in contact with LEU1128 (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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1124A LEU* 3.0 31.2 + - + +
1125A ILE* 3.8 0.4 - - - +
1127A CYS* 1.3 79.4 - - - +
1129A ALA* 1.3 65.7 + - - +
1130A GLU* 3.8 8.5 - - - +
1229A ARG* 4.1 12.8 - - - +
1231A ILE* 3.8 20.5 - - + +
1257A THR* 6.0 0.4 - - - +
1281A LEU* 3.9 24.0 - - + -
1283A TYR* 3.9 51.6 - - + +
1286A VAL* 4.5 4.3 - - - +
4119D MSE 5.0 16.2 - - + -
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Residues in contact with ALA1129 (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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1125A ILE* 2.8 22.0 + - + +
1126A MSE 3.1 8.7 + - - +
1128A LEU* 1.3 77.5 - - - +
1130A GLU* 1.3 57.6 + - - +
1131A PRO* 4.2 6.3 - - + -
1151A LEU* 5.0 4.9 - - + -
1203A ILE* 3.7 27.8 - - + +
1205A VAL* 5.4 0.4 - - + -
1229A ARG* 2.8 39.6 + - - +
1231A ILE* 3.7 13.7 - - + +
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Residues in contact with GLU1130 (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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1126A MSE 2.9 11.0 + - - -
1127A CYS 3.4 16.6 - - - +
1128A LEU 3.8 2.7 - - - +
1129A ALA* 1.3 79.9 - - - +
1131A PRO* 1.3 69.2 - - - +
1132A GLY* 3.5 1.7 + - - -
1135A ASP* 3.9 1.0 - - - +
1229A ARG* 3.0 19.3 + - - +
1286A VAL* 3.2 41.9 - - - +
4101D MSE 4.0 19.1 + - - +
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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