Contacts of the helix formed by residues 554 - 565 (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 ASP 554 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553I ASP* 1.3 75.1 - - - +
555I ALA* 1.3 75.2 + - - +
556I ASN* 3.2 26.7 + - - +
557I ARG* 3.3 4.2 + - + +
558I ALA* 3.0 21.3 + - - +
879I ARG 3.5 23.2 + - - +
880I MET* 3.3 25.1 + - + +
881I ASN* 4.5 1.0 - - - +
1042J ARG* 2.8 28.7 + - - -
1061J PHE* 3.5 11.6 - - + -
1070J TYR* 3.6 0.2 - - - -
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Residues in contact with ALA 555 (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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441I VAL* 3.9 14.3 - - + +
554I ASP* 1.3 81.6 + - - +
556I ASN* 1.3 57.9 + - - +
558I ALA* 3.7 0.9 - - - +
559I LEU* 2.9 33.6 + - - +
1042J ARG* 4.9 1.7 - - - +
1061J PHE* 5.1 0.2 - - - -
1070J TYR* 3.5 29.0 + - + -
1073J SER* 4.9 3.1 - - - +
1074J SER* 4.1 10.3 - - - +
1077J ALA* 4.6 18.2 - - + -
1078J ARG* 5.9 3.6 - - + +
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Residues in contact with ASN 556 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554I ASP* 3.2 18.6 + - - +
555I ALA* 1.3 76.7 - - - +
557I ARG* 1.3 68.2 + - - +
559I LEU* 3.1 16.0 - - - +
560I MET* 2.9 39.8 + - + +
1077J ALA* 5.4 13.9 + - - +
1081J GLY* 5.8 6.9 - - - -
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Residues in contact with ARG 557 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554I ASP* 3.3 7.4 + - + +
556I ASN* 1.3 81.8 - - + +
558I ALA* 1.3 60.1 + - - +
560I MET* 3.3 35.8 + - - +
561I GLY 2.9 23.9 + - - -
843I HIS 3.6 17.8 - - - +
844I GLY* 2.7 36.5 + - - -
845I ASN* 4.6 0.4 - - - +
846I LYS* 4.5 12.7 - - - +
879I ARG* 3.2 77.8 - - + +
881I ASN* 3.7 8.3 - - + +
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Residues in contact with ALA 558 (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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441I VAL* 5.1 7.6 - - + -
544I THR* 5.6 1.1 - - + -
547I ILE* 3.8 6.7 - - - +
550I LEU* 3.6 24.2 - - + -
553I ASP* 4.5 8.6 - - + +
554I ASP 3.0 10.8 + - - +
555I ALA* 3.7 3.1 - - - +
557I ARG* 1.3 73.9 - - - +
559I LEU* 1.3 56.3 + - - +
561I GLY* 3.3 1.1 + - - -
562I SER* 2.8 35.9 + - - -
842I ARG 5.3 0.4 - - - -
843I HIS* 4.6 3.3 + - - +
1070J TYR* 3.3 25.1 - - - +
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Residues in contact with LEU 559 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441I VAL* 3.1 37.3 - - + +
442I GLU* 5.1 1.0 - - - -
443I THR* 3.2 33.7 - - + +
444I PRO 5.5 0.4 - - - +
445I GLU* 3.6 28.0 - - + +
449I ILE* 6.2 0.7 - - + -
555I ALA 2.9 15.9 + - - +
556I ASN* 3.1 18.4 - - - +
558I ALA* 1.3 76.1 - - - +
560I MET* 1.3 58.9 + - + +
562I SER* 2.9 8.0 + - - -
563I ASN* 2.9 33.9 + - + +
1078J ARG* 4.5 13.9 - - + -
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Residues in contact with MET 560 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445I GLU* 3.2 37.0 - - + +
556I ASN* 2.9 29.8 + - + +
557I ARG* 3.4 55.4 - - - +
558I ALA 3.2 0.2 - - - -
559I LEU* 1.3 77.7 - - + +
561I GLY* 1.3 56.5 + - - +
563I ASN* 3.4 2.1 + - - +
564I MET* 2.9 39.0 + - + +
844I GLY* 4.4 2.5 - - - -
846I LYS* 3.5 28.0 - - - -
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Residues in contact with GLY 561 (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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547I ILE* 4.5 0.2 - - - -
557I ARG 2.9 14.9 + - - -
558I ALA 3.8 2.0 - - - -
560I MET* 1.3 73.7 - - - +
562I SER* 1.3 60.3 + - - +
564I MET* 2.9 31.0 + - - +
565I GLN* 3.0 20.1 + - - +
841I ASN 4.4 2.4 - - - +
842I ARG 3.8 16.2 - - - -
844I GLY* 3.7 8.4 - - - -
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Residues in contact with SER 562 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442I GLU* 3.4 12.2 + - - +
543I ASN* 3.2 29.4 + - - +
544I THR* 3.5 40.5 + - - -
547I ILE* 3.6 13.1 - - - +
558I ALA 2.8 22.8 + - - -
559I LEU* 2.9 16.3 + - - -
561I GLY* 1.3 73.5 - - - +
563I ASN* 1.3 59.5 + - - +
564I MET 3.5 0.2 + - - -
565I GLN* 3.6 8.9 + - - -
566I THR* 4.0 1.2 + - - -
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Residues in contact with ASN 563 (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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405I ARG* 3.5 6.5 + - - +
409I ARG* 2.8 31.1 + - - +
442I GLU* 4.1 5.3 + - - +
443I THR 4.0 9.6 + - - +
444I PRO* 4.0 22.6 - - - +
445I GLU* 4.2 10.0 + - - +
559I LEU* 2.9 20.0 + - + +
560I MET* 3.7 7.0 - - - +
562I SER* 1.3 77.8 + - - +
564I MET* 1.3 61.3 + - + +
565I GLN 3.4 0.2 - - - -
566I THR* 3.5 18.0 + - - -
567I GLN* 4.1 4.2 + - - +
2T C 4.8 6.1 + - - -
3T G 4.1 22.5 + - - +
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Residues in contact with MET 564 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445I GLU* 5.9 0.7 - - - +
560I MET* 2.9 26.1 + - + +
561I GLY* 2.9 17.6 + - - +
563I ASN* 1.3 75.3 - - + +
565I GLN* 1.3 56.2 + - - +
566I THR 3.0 5.6 - - - -
567I GLN* 2.9 34.3 + - - +
568I ALA* 3.4 7.8 + - - +
838I LYS* 5.4 0.4 - - - -
840I ALA* 3.6 14.8 - - + -
841I ASN 4.2 3.1 - - - +
844I GLY* 3.7 17.9 - - - -
846I LYS* 3.5 44.0 - - + +
995I MET* 5.5 0.3 - - - +
997I LEU* 3.4 37.1 - - + +
3T G 5.4 3.6 - - - +
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Residues in contact with GLN 565 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I ASN* 3.6 9.4 + - - +
401I LEU* 3.6 13.6 - - + +
543I ASN* 3.5 24.7 + - - +
546I LEU* 3.5 30.9 - - - +
547I ILE* 3.6 15.0 - - - +
561I GLY 3.0 16.8 + - - +
562I SER 3.7 8.5 - - - +
563I ASN 3.4 0.6 - - - -
564I MET* 1.3 76.1 - - - +
566I THR* 1.3 57.7 + - - +
567I GLN 3.4 0.2 - - - -
568I ALA* 3.2 19.2 - - - +
668I LEU* 3.7 27.6 - - + +
841I ASN 6.0 0.4 - - - +
842I ARG* 3.4 34.6 - - + +
995I MET* 5.8 0.7 - - - -
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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