Contacts of the helix formed by residues 521 - 538 (chain E) in PDB entry 1XFV
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 ASN 521 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519E THR* 3.9 3.4 - - - +
520E PRO* 1.3 83.6 - - + +
522E SER* 1.3 63.4 + - - +
523E LEU* 4.2 12.5 + - - +
524E GLU* 3.2 32.6 + - + +
525E LYS* 2.8 27.5 + - - +
127S GLU* 4.6 7.6 - - - +
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Residues in contact with SER 522 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520E PRO 2.9 11.3 + - - -
521E ASN* 1.3 71.7 + - - +
523E LEU* 1.3 66.2 + - - +
525E LYS* 2.8 19.5 + - - -
526E GLN 3.0 0.2 + - - -
120S GLU* 4.2 23.0 + - - +
123S GLN* 4.4 17.7 + - - +
124S MET* 3.0 39.3 - - - +
127S GLU* 5.4 0.7 - - - -
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Residues in contact with LEU 523 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521E ASN* 3.3 7.1 + - - +
522E SER* 1.3 78.1 - - - +
524E GLU* 1.3 62.0 + - - +
526E GLN* 3.3 16.8 + - - +
527E LYS* 3.3 20.1 + - - +
124S MET* 4.7 7.8 - - - +
127S GLU* 3.3 53.6 + - + +
128S ALA* 4.6 12.1 - - + +
144S MET* 3.5 38.4 - - + +
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Residues in contact with GLU 524 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516E VAL* 5.4 0.2 - - - +
519E THR* 3.7 17.7 + - - +
521E ASN* 3.0 34.7 + - + +
523E LEU* 1.3 77.8 - - - +
525E LYS* 1.3 59.3 + - - +
527E LYS* 3.4 25.7 + - - +
528E GLY* 2.8 30.8 + - - -
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Residues in contact with LYS 525 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516E VAL* 4.6 2.0 - - - +
517E VAL* 2.9 40.1 + - - +
519E THR* 3.4 28.7 - - + +
521E ASN 2.8 9.2 + - - +
522E SER* 2.8 14.5 + - - +
524E GLU* 1.3 73.8 - - - +
526E GLN* 1.3 61.2 + - - +
528E GLY* 4.1 1.1 - - - +
529E VAL* 2.9 37.5 + - + +
109S MET* 4.3 3.8 - - + -
114S GLU* 2.5 51.9 + - - -
116S LEU* 3.7 14.1 - - + -
120S GLU* 6.2 0.2 - - - +
124S MET* 4.1 12.8 - - + -
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Residues in contact with GLN 526 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522E SER 3.0 6.0 + - - +
523E LEU* 3.6 17.9 - - - +
524E GLU 3.2 0.4 - - - -
525E LYS* 1.3 74.9 - - - +
527E LYS* 1.3 69.8 + - - +
529E VAL* 3.1 6.4 + - - +
530E THR* 2.9 26.8 + - - +
92S PHE* 5.3 4.9 - - + -
100S ILE* 5.6 5.1 - - - +
105S LEU* 3.3 35.8 - - + +
109S MET* 5.2 6.5 - - - -
124S MET* 3.4 31.5 - - + +
125S ILE* 5.7 2.0 - - - +
128S ALA* 4.6 7.7 - - - +
136S VAL* 5.8 3.2 - - - +
141S PHE* 4.3 10.3 - - - -
144S MET* 3.5 29.3 - - + +
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Residues in contact with LYS 527 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523E LEU 3.3 9.1 + - - +
524E GLU* 3.7 29.0 + - - +
526E GLN* 1.3 77.1 - - - +
528E GLY* 1.3 70.1 + - - +
530E THR* 2.7 16.3 + - - -
531E ASN* 3.1 30.9 + - - +
144S MET* 4.1 13.2 - - - +
145S MET* 3.0 48.8 + - - +
146S THR 5.4 0.4 + - - -
147S ALA 4.6 7.4 + - - +
148S LYS* 4.7 17.8 + - - +
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Residues in contact with GLY 528 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516E VAL* 3.9 21.0 - - - +
524E GLU* 2.8 21.3 + - - -
527E LYS* 1.3 78.3 - - - +
529E VAL* 1.3 60.2 + - - +
531E ASN* 3.7 8.9 + - - +
532E LEU* 3.3 22.9 + - - +
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Residues in contact with VAL 529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513E TRP* 4.7 18.4 - - + +
516E VAL* 4.6 8.3 - - + -
517E VAL* 5.0 7.4 - - + -
525E LYS* 2.9 30.5 + - + +
526E GLN 3.1 4.2 + - - +
527E LYS 2.8 4.8 + - - -
528E GLY* 1.3 70.1 - - - +
530E THR* 1.3 59.5 + - - +
532E LEU* 2.7 36.2 + - + +
533E LEU 2.9 5.4 + - - -
92S PHE* 5.2 3.6 - - + -
109S MET* 3.9 37.5 - - + -
112S LEU* 4.2 23.6 - - + -
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Residues in contact with THR 530 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526E GLN* 2.9 20.3 + - - +
527E LYS 2.7 10.9 + - - -
529E VAL* 1.3 73.6 - - - +
531E ASN* 1.3 52.5 + - - +
533E LEU* 2.9 9.3 + - - +
534E ILE* 2.7 40.1 + - + +
88S ALA* 3.5 29.6 - - + -
92S PHE* 3.9 25.9 - - + -
141S PHE* 4.2 1.1 - - + -
144S MET* 4.7 0.2 - - - +
145S MET* 3.3 35.2 - - + +
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Residues in contact with ASN 531 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527E LYS* 3.1 40.4 + - - +
528E GLY* 3.9 8.9 - - - +
530E THR* 1.3 77.9 - - - +
532E LEU* 1.3 56.8 - - - +
534E ILE* 3.5 20.7 - - + +
535E LYS* 2.7 32.5 + - - +
85S ILE* 5.1 4.5 - - - +
145S MET* 4.6 11.4 - - - +
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Residues in contact with LEU 532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508E ILE* 3.9 14.8 - - + -
512E GLU* 4.1 9.9 - - + +
513E TRP* 3.4 43.3 - - + +
516E VAL* 3.9 22.0 - - + -
528E GLY 3.3 11.9 + - - +
529E VAL* 2.7 22.9 + - + +
531E ASN* 1.3 71.0 - - - +
533E LEU* 1.3 57.5 + - - +
535E LYS* 3.0 4.6 + - + +
536E TYR* 2.7 66.4 + - + +
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Residues in contact with LEU 533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501E LEU* 4.1 12.1 - - + -
504E ILE* 4.4 13.0 - - + +
508E ILE* 5.0 3.3 - - - +
529E VAL 2.9 6.7 + - - +
530E THR* 2.9 9.6 + - - +
532E LEU* 1.3 74.4 - - - +
534E ILE* 1.3 62.4 + - - +
537E GLY* 3.0 17.9 + - - +
538E ILE* 3.3 19.8 + - + -
625E LEU* 3.8 28.0 - - + -
88S ALA* 4.6 4.0 - - + -
91S VAL* 4.0 26.0 - - + -
92S PHE* 4.0 19.5 - - + -
112S LEU* 3.8 28.7 - - + +
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Residues in contact with ILE 534 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530E THR* 2.7 25.4 + - + +
531E ASN* 3.5 20.9 - - - +
533E LEU* 1.3 71.7 - - - +
535E LYS* 1.3 66.0 + - - +
538E ILE* 2.7 38.7 + - + -
539E GLU* 2.9 12.5 + - + +
84S GLU* 4.0 24.9 - - + +
85S ILE* 3.8 42.8 - - + +
88S ALA* 3.9 20.2 - - + -
145S MET* 5.7 0.4 - - + -
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Residues in contact with LYS 535 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512E GLU* 4.2 5.5 + - - -
531E ASN 2.7 23.7 + - - +
532E LEU* 3.3 5.8 - - + +
534E ILE* 1.3 81.8 - - + +
536E TYR* 1.3 107.2 + - + +
537E GLY 3.3 2.8 + - - -
539E GLU* 3.9 27.4 + - - +
541E LYS* 6.2 0.2 - - - -
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Residues in contact with TYR 536 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504E ILE* 4.5 4.6 - - + +
507E GLN* 3.3 43.7 - - + +
508E ILE* 3.5 36.6 - - + -
509E PRO* 3.5 16.7 - - + +
512E GLU* 2.5 41.1 + - - -
532E LEU* 2.7 29.5 + - + +
533E LEU 4.0 0.4 - - - -
535E LYS* 1.3 105.9 + - + +
537E GLY* 1.3 55.1 + - - -
550E SER* 5.7 0.4 - - - -
552E TRP* 4.2 5.5 + - - -
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Residues in contact with GLY 537 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504E ILE* 4.4 14.4 - - - -
533E LEU 3.0 11.8 + - - -
535E LYS 3.3 2.2 + - - -
536E TYR* 1.3 80.1 - - - +
538E ILE* 1.3 63.6 + - - +
539E GLU 3.8 0.4 - - - -
550E SER* 4.4 2.5 + - - -
552E TRP* 3.0 33.3 + - - -
625E LEU* 3.7 14.5 - - - +
627E TYR* 5.6 3.8 - - - -
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Residues in contact with ILE 538 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E LEU* 3.6 28.0 - - + +
534E ILE* 2.7 34.1 + - + +
537E GLY* 1.3 75.3 - - - +
539E GLU* 1.3 65.5 + - - +
540E ARG* 3.2 21.6 + - - +
550E SER* 5.2 0.7 - - - -
625E LEU* 4.3 9.9 - - + -
627E TYR* 5.0 12.4 - - + -
84S GLU* 4.6 9.6 - - + +
87S GLU* 3.5 33.0 - - + +
88S ALA* 3.7 32.8 - - - +
91S VAL* 4.8 5.2 - - + -
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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
------------------------------------------------------------
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