Contacts of the helix formed by residues 1220 - 1231 (chain N) in PDB entry 5D4D
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 ALA1220 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041M GLU 3.6 23.8 + - - +
1042M ALA* 4.6 3.0 + - - -
1044M GLY* 5.5 1.2 - - - -
1105N ILE 4.6 1.1 - - - +
1106N VAL* 3.8 22.9 - - + -
1218N GLY 3.4 2.4 + - - -
1219N GLU* 1.3 75.1 - - - +
1221N VAL* 1.3 61.0 - - - +
1222N GLY 3.3 2.3 + - - -
1223N ILE* 3.8 7.4 + - + +
1224N VAL* 3.2 24.4 + - - +
1462N LEU* 4.3 13.7 - - + -
1474N ALA* 4.0 10.5 - - + -
1475N GLY 5.2 0.2 - - - +
17O TYR* 4.9 0.4 + - - -
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Residues in contact with VAL1221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105N ILE* 3.4 29.0 + - + +
1106N VAL* 4.4 2.5 - - - +
1107N VAL* 3.7 24.0 - - + -
1200N VAL* 3.9 15.9 - - + -
1205N TYR* 3.5 39.1 + - + +
1215N VAL* 4.7 0.2 - - + -
1219N GLU* 3.2 14.5 + - + +
1220N ALA* 1.3 72.3 - - - +
1222N GLY* 1.3 63.2 + - - +
1223N ILE 3.5 0.2 - - - -
1224N VAL* 3.7 8.6 - - - +
1225N ALA* 2.9 29.5 + - - +
1370N ILE* 4.1 10.1 - - + +
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Residues in contact with GLY1222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102N THR* 2.9 45.8 + - - -
1105N ILE* 3.0 17.3 + - - -
1221N VAL* 1.3 77.3 - - - +
1223N ILE* 1.3 60.3 + - - +
1225N ALA* 3.0 7.1 + - - +
1226N ALA 2.9 19.9 + - - -
1370N ILE* 4.4 2.7 - - - -
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Residues in contact with ILE1223 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038M TRP* 3.6 33.0 - - + +
1041M GLU* 3.6 20.4 - - + +
1042M ALA* 4.3 6.1 - - + -
1099N VAL* 3.8 15.7 - - + -
1103N HIS* 3.7 32.5 - - + +
1220N ALA* 3.8 10.9 + - + +
1222N GLY* 1.3 73.8 - - - +
1224N VAL* 1.3 58.6 + - - +
1226N ALA* 3.3 5.9 + - - +
1227N GLN* 2.9 43.8 + - + +
1462N LEU* 3.6 21.3 - - + -
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Residues in contact with VAL1224 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042M ALA* 4.0 21.5 - - + +
710N ARG* 4.2 7.0 - - - +
772N PRO* 4.0 21.3 - - + +
1205N TYR* 4.5 5.8 - - - +
1219N GLU* 4.0 19.3 - - + +
1220N ALA 3.2 17.4 + - - +
1221N VAL* 3.5 10.7 + - - +
1222N GLY 3.2 0.6 - - - -
1223N ILE* 1.3 77.4 - - - +
1225N ALA* 1.3 56.2 + - - +
1227N GLN* 3.8 7.3 - - - +
1228N SER* 2.7 46.4 + - - +
1367N HIS* 4.1 13.2 - - + -
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Residues in contact with ALA1225 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221N VAL 2.9 15.0 + - - +
1222N GLY 3.3 9.4 - - - +
1224N VAL* 1.3 75.1 - - - +
1226N ALA* 1.3 66.3 + - - +
1228N SER* 3.2 1.4 + - - -
1229N ILE* 2.9 33.0 + - + +
1367N HIS* 3.7 42.2 - - - +
1370N ILE* 4.1 13.7 - - + -
1371N VAL* 4.8 2.9 - - + -
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Residues in contact with ALA1226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095N THR* 4.1 5.3 - - - +
1098N LEU* 3.7 20.6 - - + +
1099N VAL* 3.5 47.3 - - + +
1102N THR* 3.8 1.3 + - - +
1222N GLY 2.9 11.2 + - - +
1223N ILE 3.3 6.0 + - - +
1225N ALA* 1.3 77.7 - - - +
1227N GLN* 1.3 56.9 + - - +
1229N ILE* 3.4 2.6 + - - +
1230N GLY* 2.9 26.9 + - - -
1371N VAL* 5.2 1.3 - - - +
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Residues in contact with GLN1227 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035M MET 4.6 2.0 + - - -
1038M TRP* 3.4 46.5 + - + +
1039M ALA* 3.7 6.9 - - - +
1042M ALA* 3.4 20.3 - - - +
707N THR 5.6 1.2 + - - -
708N LEU 3.5 21.0 + - - +
709N HIS* 3.8 13.3 - - + +
710N ARG* 3.5 17.7 + - - +
1095N THR* 5.0 3.6 - - + -
1099N VAL* 5.3 4.3 - - + -
1223N ILE* 2.9 22.8 + - + +
1224N VAL* 4.0 5.4 - - - +
1226N ALA* 1.3 75.6 - - + +
1228N SER* 1.3 60.9 + - - +
1230N GLY* 4.4 0.7 - - - +
1231N GLU* 2.9 36.2 + - - +
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Residues in contact with SER1228 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709N HIS* 5.7 1.3 - - - -
772N PRO* 4.1 1.2 - - - +
773N ALA* 3.4 41.9 + - - +
1224N VAL* 2.7 28.7 + - - +
1225N ALA 3.7 3.1 - - - -
1227N GLN* 1.3 77.5 - - - +
1229N ILE* 1.3 60.0 + - - +
1231N GLU* 4.7 2.1 - - - +
1232N PRO* 3.5 15.9 - - - +
1363N LEU* 3.3 23.5 - - - +
1367N HIS* 3.8 12.9 - - - -
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Residues in contact with ILE1229 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094N LEU* 5.3 1.3 - - + -
1098N LEU* 3.7 14.4 - - + -
1225N ALA 2.9 21.1 + - - +
1228N SER* 1.3 79.0 - - - +
1230N GLY* 1.3 62.8 + - - +
1232N PRO* 3.4 10.0 - - - +
1233N GLY* 4.5 1.6 + - - -
1263N PHE* 3.6 32.1 - - + -
1356N TYR* 2.9 43.7 + - + +
1363N LEU* 4.0 13.0 - - + -
1367N HIS* 3.9 22.0 - - + +
1368N ILE* 4.0 9.4 - - + +
1371N VAL* 3.6 30.3 - - + -
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Residues in contact with GLY1230 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708N LEU* 5.8 1.6 - - - +
1091N SER* 3.6 7.8 + - - -
1094N LEU* 5.6 4.9 - - - -
1095N THR* 3.2 28.4 + - - -
1098N LEU* 4.5 2.2 - - - +
1226N ALA 2.9 15.7 + - - -
1229N ILE* 1.3 79.5 - - - +
1231N GLU* 1.3 55.0 + - - +
1233N GLY* 2.6 31.8 + - - -
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Residues in contact with GLU1231 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708N LEU* 3.7 46.8 + - + +
709N HIS* 3.3 37.9 - - + +
1227N GLN* 2.9 19.7 + - - +
1228N SER* 4.7 2.0 - - - +
1230N GLY* 1.3 74.7 - - - +
1232N PRO* 1.3 82.1 - - + +
1233N GLY 3.1 4.0 + - - -
1234N THR* 4.3 6.4 + - - +
1235N GLN* 5.7 3.0 + - - +
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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