Contacts of the helix formed by residues 1038 - 1051 (chain B) in PDB entry 4Z4Q
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 LYS1038 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028B ARG 3.6 14.1 - - - +
1029B ALA* 2.9 28.3 - - - +
1030B LEU* 4.1 0.7 - - - +
1031B PRO* 4.0 16.4 - - + -
1037B LEU* 1.3 75.2 - - - +
1039B PRO* 1.3 76.9 - - + +
1040B VAL* 3.2 10.1 - - + +
1041B GLN* 2.8 43.2 + - + +
1042B ARG* 3.1 10.9 + - - +
1167B SER* 4.1 12.9 + - - +
1168B THR 2.5 35.0 + - - +
1169B GLY 3.5 1.4 - - - +
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Residues in contact with PRO1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026B GLN 4.3 3.6 - - - +
1027B ASP* 3.5 41.7 - - + +
1028B ARG* 3.8 17.5 - - - +
1030B LEU 4.6 6.7 - - - +
1037B LEU 4.7 0.7 - - - +
1038B LYS* 1.3 87.3 - - + +
1040B VAL* 1.3 63.6 + - - +
1042B ARG* 3.2 22.9 + - - +
1043B ARG* 3.0 49.6 + - - +
1074B HIS* 5.3 1.1 - - + -
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Residues in contact with VAL1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B ARG 5.9 0.4 - - - +
1038B LYS* 4.6 10.5 - - + -
1039B PRO* 1.3 81.5 - - - +
1041B GLN* 1.3 80.4 + - + +
1043B ARG* 3.5 2.8 + - + +
1044B ILE* 3.1 35.0 + - + +
1069B ILE* 5.8 0.2 - - + -
1074B HIS* 3.5 42.4 - - + +
1080B SER* 5.0 2.0 - - - +
1081B ILE* 4.4 15.5 - - + +
1084B ALA* 4.0 15.3 - - + -
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Residues in contact with GLN1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036B GLY 4.1 3.3 - - - +
1037B LEU* 3.3 25.9 - - + +
1038B LYS* 2.8 51.5 + - - +
1040B VAL* 1.3 89.5 - - + +
1042B ARG* 1.3 66.3 + - - +
1044B ILE* 3.2 4.8 + - - +
1045B LEU* 2.9 28.5 + - - +
1084B ALA* 5.1 5.5 + - + +
1087B ARG* 5.5 8.3 - - - +
1088B MET* 3.8 32.1 - - + +
1167B SER* 5.6 2.1 + - - -
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Residues in contact with ARG1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032B ASP* 3.3 17.8 - - - +
1035B ASP* 2.9 28.2 + - - -
1037B LEU* 2.9 39.1 + - + +
1038B LYS 3.1 5.8 + - - +
1039B PRO* 3.6 26.2 - - - +
1041B GLN* 1.3 75.3 - - - +
1043B ARG* 1.3 60.5 + - + +
1045B LEU* 3.3 3.7 + - - +
1046B TYR* 2.8 30.8 + - - +
1152B PRO* 3.9 14.6 + - + +
1153B THR* 3.5 17.9 + - - +
1154B VAL* 3.6 26.8 - - - +
1155B LEU* 3.7 22.7 - - + +
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Residues in contact with ARG1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023B TYR* 5.4 3.6 + - - -
1027B ASP* 5.8 1.2 + - - -
1039B PRO* 3.0 30.1 + - - +
1040B VAL* 3.9 3.4 - - - +
1042B ARG* 1.3 76.3 - - + +
1044B ILE* 1.3 61.3 + - - +
1046B TYR* 4.3 5.4 - - + +
1047B SER* 2.8 36.2 + - - -
1069B ILE* 4.5 10.5 - - + -
1073B PHE* 3.4 37.5 + - + -
1074B HIS* 2.9 38.4 + - + +
1075B PRO* 4.6 6.0 - - - +
1076B HIS* 5.3 1.6 + - - -
1151B GLU* 2.9 42.5 + - + +
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Residues in contact with ILE1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B VAL* 3.1 23.6 + - + +
1041B GLN* 3.6 8.1 - - - +
1043B ARG* 1.3 74.7 - - - +
1045B LEU* 1.3 62.5 + - + +
1047B SER* 4.1 0.3 - - - -
1048B MET* 3.1 45.1 + - - +
1069B ILE* 3.7 24.4 - - + +
1081B ILE* 3.8 14.4 - - + +
1084B ALA* 3.7 16.6 - - + -
1085B MET* 3.6 34.8 - - + +
1088B MET* 3.2 30.1 - - + -
1099B VAL* 4.7 0.4 - - + -
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Residues in contact with LEU1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037B LEU* 3.8 18.2 - - + -
1041B GLN 2.9 18.2 + - - +
1042B ARG 3.7 4.0 - - - +
1044B ILE* 1.3 74.9 - - - +
1046B TYR* 1.3 66.2 + - - +
1048B MET 3.9 0.2 - - - -
1049B ASN* 3.0 25.5 + - - +
1088B MET* 4.1 20.4 - - + -
1098B LEU* 4.3 23.1 - - + +
1099B VAL* 4.5 0.2 - - + -
1123B LEU* 3.8 26.2 - - + +
1127B ALA* 4.7 6.1 - - + -
1130B LEU* 3.6 32.8 - - + -
1131B LEU* 3.8 9.5 - - + +
1155B LEU* 4.2 12.3 - - + -
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Residues in contact with TYR1046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042B ARG 2.8 21.7 + - - +
1043B ARG* 4.0 4.5 - - - +
1045B LEU* 1.3 73.0 - - - +
1047B SER* 1.3 65.2 + - - +
1049B ASN* 3.2 4.9 + - - +
1050B LYS* 2.9 42.6 + - + +
1073B PHE* 3.7 35.7 - + - -
1131B LEU* 4.6 9.0 - - + -
1134B ILE* 3.9 26.2 - - + -
1141B PHE* 3.8 14.4 - + - -
1149B GLU* 5.3 1.0 + - - +
1150B LYS 3.8 12.0 + - - -
1151B GLU* 4.7 0.7 - - + -
1152B PRO* 3.6 44.0 - - + -
1155B LEU* 5.0 2.7 - - + -
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Residues in contact with SER1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043B ARG 2.8 18.3 + - - -
1046B TYR* 1.3 78.3 - - - +
1048B MET* 1.3 64.6 + - - +
1049B ASN 2.9 1.0 + - - -
1050B LYS* 3.0 16.1 + - - +
1051B ASP* 3.1 24.6 + - - -
1065B SER 4.7 1.0 + - - -
1068B ASN* 4.1 4.9 - - - +
1069B ILE* 3.5 31.8 + - - +
1072B ASN* 5.0 1.0 + - - -
1073B PHE* 3.9 25.9 - - - -
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Residues in contact with MET1048 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044B ILE* 3.1 37.6 + - + +
1047B SER* 1.3 79.5 - - - +
1049B ASN* 1.3 60.6 + - - +
1051B ASP* 3.4 3.9 + - - -
1052B SER 3.4 2.1 + - - -
1053B ASN* 2.9 60.3 + - + +
1065B SER* 4.3 14.4 - - - +
1069B ILE* 4.9 4.0 - - + -
1085B MET* 4.5 14.8 - - - +
1099B VAL* 4.7 6.1 - - + -
1121B ALA* 4.2 6.3 - - + -
1122B ARG* 3.5 36.1 - - - +
1123B LEU* 3.6 21.8 - - + +
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Residues in contact with ASN1049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B LEU 3.0 8.7 + - - +
1046B TYR* 3.8 5.0 - - + +
1047B SER 3.0 1.0 - - - -
1048B MET* 1.3 76.7 - - - +
1050B LYS* 1.3 65.1 + - - +
1052B SER* 2.9 14.4 + - - -
1054B THR* 3.6 24.2 - - - +
1123B LEU* 3.6 7.8 - - + +
1128B GLY* 5.5 4.9 - - - -
1131B LEU* 3.3 46.0 - - + +
1134B ILE* 4.5 12.0 - - - +
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Residues in contact with LYS1050 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046B TYR* 2.9 32.4 + - + +
1047B SER* 3.4 11.0 - - - +
1049B ASN* 1.3 76.2 + - - +
1051B ASP* 1.3 68.2 + - - +
1052B SER* 3.3 8.7 + - - -
1072B ASN* 6.0 1.3 - - - +
1073B PHE* 4.6 11.4 - - + -
1149B GLU* 3.0 28.3 - - - +
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Residues in contact with ASP1051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047B SER* 3.1 17.8 + - - +
1048B MET* 3.9 6.9 - - - +
1049B ASN 3.1 0.8 - - - -
1050B LYS* 1.3 90.5 - - - +
1052B SER* 1.3 72.1 + - - +
1053B ASN* 3.0 3.4 + - + -
1060B ARG* 3.4 34.4 + - - +
1065B SER* 6.0 0.3 - - - -
1068B ASN* 3.2 33.8 + - - +
1072B ASN* 5.6 1.6 + - - -
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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