Contacts of the helix formed by residues 1059 - 1072 (chain I) in PDB entry 4XLN
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 ASP1059 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054I THR* 3.1 30.6 + - + +
1055I ILE* 4.4 0.2 - - - -
1057I SER 3.7 0.8 - - - -
1058I ASP* 1.3 76.9 + - - +
1060I ILE* 1.3 74.8 + - - +
1061I GLU* 2.8 17.8 - - - +
1062I GLY* 3.1 23.1 + - - -
1063I ARG* 2.5 31.1 + - - +
1079I PRO* 3.1 29.3 - - - +
1080I SER 3.8 0.6 + - - -
1081I VAL 2.7 32.1 + - - +
1082I PRO 4.4 0.7 - - - -
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Residues in contact with ILE1060 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018I GLN* 4.8 6.7 - - + -
1058I ASP 3.3 1.8 + - - +
1059I ASP* 1.3 88.4 + - - +
1061I GLU* 1.3 72.9 + - + +
1063I ARG* 3.4 10.7 + - - +
1064I ASN* 3.3 23.8 + - - +
1081I VAL* 3.7 11.2 + - + +
1083I GLU* 3.2 30.0 - - + +
1086I ARG* 3.3 22.2 - - - +
1113I GLU* 3.4 22.0 - - - +
84J ILE* 5.6 7.6 - - + -
88J TYR* 4.7 1.1 - - - +
353L LEU* 5.1 11.6 - - + +
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Residues in contact with GLU1061 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059I ASP* 2.8 31.1 - - - +
1060I ILE* 1.3 86.7 - - + +
1062I GLY* 1.3 64.8 + - - +
1063I ARG 3.5 0.4 - - - -
1064I ASN* 3.9 10.1 - - + +
1065I ALA* 2.9 37.8 + - + +
1078I GLU 5.6 0.5 - - - +
1079I PRO* 5.0 2.7 - - - -
1080I SER* 2.9 27.8 + - - -
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Residues in contact with GLY1062 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055I ILE* 3.8 15.5 - - - +
1059I ASP* 3.1 26.0 + - - -
1060I ILE 3.2 2.2 - - - -
1061I GLU* 1.3 84.0 + - - +
1063I ARG* 1.3 56.2 + - - +
1065I ALA* 4.4 1.0 - - - +
1066I ALA* 2.9 32.3 + - - +
1079I PRO* 5.1 2.9 - - - -
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Residues in contact with ARG1063 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010I THR* 6.1 0.2 - - - +
1013I TYR* 3.2 50.4 - - - -
1018I GLN* 3.7 27.0 + - - +
1055I ILE* 3.3 20.6 + - - +
1056I LYS* 5.1 0.4 - - - -
1057I SER 4.2 7.9 - - - -
1058I ASP 3.5 10.3 + - - -
1059I ASP 2.5 44.1 + - - +
1060I ILE* 3.4 12.1 - - - +
1062I GLY* 1.3 73.1 - - - +
1064I ASN* 1.3 68.5 + - - +
1066I ALA* 3.8 3.9 - - - +
1067I TYR* 2.9 29.5 + - - +
624J ASP* 4.0 12.8 - - - +
625J TYR* 4.3 8.5 + - + +
353L LEU* 3.7 15.6 - - - +
354L PRO 4.8 6.7 + - - -
356L PRO* 3.5 13.2 - - + +
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Residues in contact with ASN1064 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060I ILE 3.3 18.6 + - - +
1061I GLU* 3.5 10.1 + - + +
1062I GLY 3.2 0.6 - - - -
1063I ARG* 1.3 77.0 + - - +
1065I ALA* 1.3 61.5 + - - +
1066I ALA 3.1 0.9 - - - -
1067I TYR* 3.0 5.4 + - - +
1068I GLN* 2.9 28.2 + - - +
354L PRO* 4.2 19.5 + - - +
355L SER 4.5 0.2 + - - -
356L PRO* 3.3 36.5 - - - +
359L ALA* 3.6 27.3 - - + +
360L ALA* 5.5 0.2 - - - +
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Residues in contact with ALA1065 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061I GLU* 2.9 29.8 + - + +
1062I GLY 4.4 1.1 - - - +
1064I ASN* 1.3 73.1 - - - +
1066I ALA* 1.3 56.4 + - - +
1068I GLN* 3.5 13.6 + - - +
1069I ALA* 2.9 28.8 + - - +
1077I PRO* 4.4 18.3 - - + +
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Residues in contact with ALA1066 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055I ILE* 3.7 20.6 - - + -
1062I GLY 2.9 22.3 + - - +
1063I ARG* 3.8 5.2 - - - +
1065I ALA* 1.3 73.9 - - - +
1067I TYR* 1.3 66.0 + - - +
1069I ALA* 2.9 4.2 + - - +
1070I ILE* 2.9 29.9 + - + +
1076I VAL* 3.6 26.5 - - + -
1077I PRO* 5.0 1.2 - - - +
625J TYR* 5.1 2.2 - - + +
751J LEU* 4.8 6.3 - - + -
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Residues in contact with TYR1067 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010I THR* 4.4 6.5 - - - -
1063I ARG 2.9 20.7 + - - +
1064I ASN 3.4 3.8 - - - +
1066I ALA* 1.3 74.6 - - - +
1068I GLN* 1.3 56.8 + - - +
1070I ILE* 3.4 4.3 + - - +
1071I ILE* 2.9 61.5 + - + +
625J TYR* 4.0 13.2 + - - +
654J LYS* 5.9 1.0 - - + -
655J PRO* 3.9 27.1 - - + -
658J LEU* 5.0 6.1 - - - +
670J VAL* 5.5 1.8 - - + +
674J ARG* 3.7 18.9 + - - -
356L PRO* 3.4 21.3 - - + +
357L VAL* 3.6 37.1 - - + +
360L ALA* 3.5 24.2 - - + -
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Residues in contact with GLN1068 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064I ASN 2.9 15.6 + - - +
1065I ALA* 3.8 11.9 - - - +
1067I TYR* 1.3 73.7 - - - +
1069I ALA* 1.3 61.5 + - - +
1071I ILE* 3.4 5.9 + - - -
1072I LYS* 2.9 66.9 + - + +
1074I GLU* 4.5 0.9 - - - +
359L ALA 6.0 0.2 - - - -
360L ALA* 4.4 17.0 - - + +
363L SER* 3.5 29.3 + - - -
367L GLU* 4.0 2.4 + - - -
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Residues in contact with ALA1069 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065I ALA 2.9 18.4 + - - +
1066I ALA 2.9 5.4 + - - +
1068I GLN* 1.3 77.6 - - - +
1070I ILE* 1.3 54.8 + - - +
1072I LYS 3.6 0.2 - - - -
1073I GLY 2.9 7.8 + - - -
1074I GLU* 2.6 54.0 + - + +
1075I ASP 4.2 1.6 - - - +
1076I VAL* 3.8 30.1 - - + +
1077I PRO* 4.3 4.3 - - + -
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Residues in contact with ILE1070 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066I ALA 2.9 21.9 + - - +
1067I TYR* 3.8 3.4 - - - +
1069I ALA* 1.3 73.5 - - - +
1071I ILE* 1.3 66.6 + - - +
1073I GLY* 3.2 9.6 + - - -
1074I GLU 4.6 4.9 - - - +
1076I VAL* 3.9 15.5 - - + -
625J TYR* 4.2 17.9 - - + +
655J PRO* 3.6 39.5 - - + -
656J PHE* 3.7 45.5 - - + -
659J LYS* 3.4 14.6 - - - +
751J LEU* 4.7 11.2 - - + -
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Residues in contact with ILE1071 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067I TYR* 2.9 63.3 + - + +
1068I GLN* 3.8 8.5 - - - +
1070I ILE* 1.3 76.2 - - - +
1072I LYS* 1.3 70.8 + - + +
655J PRO* 3.5 26.7 - - + +
658J LEU* 4.5 5.8 - - + -
659J LYS* 3.2 25.7 + - - +
662J GLU* 5.4 0.2 - - - +
670J VAL* 3.7 45.6 - - + +
360L ALA* 5.1 4.0 - - + -
364L LEU* 4.6 9.4 - - + -
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Residues in contact with LYS1072 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068I GLN* 2.9 56.3 + - + +
1070I ILE 3.2 0.2 - - - -
1071I ILE* 1.3 86.1 - - + +
1073I GLY* 1.3 63.1 + - - +
1074I GLU* 3.5 28.2 - - - +
659J LYS* 3.8 14.8 + - - +
360L ALA* 5.6 1.4 + - - +
363L SER* 5.0 0.6 - - - -
364L LEU* 5.0 11.5 - - - +
367L GLU* 3.7 26.4 + - - -
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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