Contacts of the helix formed by residues 555 - 571 (chain A) in PDB entry 3IAY
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 GLY 555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A PHE* 4.1 8.4 - - - -
446A TYR* 4.6 3.4 - - - -
470A ARG* 4.6 4.7 - - - -
550A TYR 5.1 1.0 - - - +
554A ARG* 1.3 79.3 - - - +
556A GLN* 1.3 66.5 + - - -
557A GLN 3.4 1.8 - - - -
558A ILE* 3.5 18.0 - - - +
559A LYS* 3.8 10.7 - - - +
3T A 3.3 11.8 + - - -
4T G 3.4 17.4 + - - -
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Residues in contact with GLN 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ALA* 6.3 0.2 - - + -
446A TYR* 3.3 26.1 + - + +
555A GLY* 1.3 73.2 - - - -
557A GLN* 1.3 65.9 + - - +
559A LYS* 2.9 40.4 + - - +
560A VAL* 3.2 22.6 + - - +
699A ALA 5.6 0.8 + - - -
702A ILE* 3.5 21.2 - - - +
703A SER* 4.1 4.4 + - - -
706A SER* 3.3 35.0 + - - +
4T G 2.9 35.3 + - + +
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Residues in contact with GLN 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A GLN* 1.3 77.6 - - - +
558A ILE* 1.3 57.7 + - - +
560A VAL* 3.1 6.6 + - - +
561A VAL* 2.8 32.5 + - - +
710A PHE* 3.6 34.7 + - + -
713A ALA* 4.0 6.0 - - - +
715A VAL 3.0 22.5 - - - +
716A GLY* 3.5 22.4 - - - -
717A LYS 4.2 1.8 - - - +
1T T 3.5 25.9 + - - +
3T A 4.2 5.5 - - - +
4T G 2.9 50.0 + - - +
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Residues in contact with ILE 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 4.1 18.8 - - + -
546A VAL* 3.7 4.3 - - + +
550A TYR* 3.6 41.7 - - + +
554A ARG* 3.9 43.1 - - + +
555A GLY 3.5 17.2 - - - +
557A GLN* 1.3 74.5 - - - +
559A LYS* 1.3 65.7 + - + +
561A VAL* 4.1 11.9 - - + -
562A SER* 2.9 28.8 + - - -
1T T 3.9 20.7 + - - +
3T A 4.4 3.3 + - - +
4T G 4.6 0.2 + - - -
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Residues in contact with LYS 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A MET* 3.6 20.5 - - - +
544A THR* 3.8 36.0 - - + +
546A VAL* 3.8 21.1 - - + -
550A TYR* 6.1 0.2 - - + -
551A LEU* 4.3 11.8 - - + +
555A GLY 3.8 16.2 - - - +
556A GLN* 2.9 37.7 + - - +
557A GLN 3.2 0.2 - - - -
558A ILE* 1.3 78.6 - - + +
560A VAL* 1.3 65.2 + - + +
562A SER* 3.5 1.9 + - - -
563A GLN* 2.9 32.1 + - - +
699A ALA 5.1 0.4 + - - -
703A SER* 3.0 21.4 + - - +
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Residues in contact with VAL 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A GLN 3.2 15.4 + - - +
557A GLN* 3.1 7.7 + - - +
559A LYS* 1.3 76.6 - - + +
561A VAL* 1.3 56.9 + - - +
563A GLN* 3.3 12.0 + - - +
564A LEU* 2.9 32.5 + - + +
663A LEU* 5.7 4.3 - - + -
666A ILE* 5.1 3.3 - - + +
703A SER 5.0 1.3 - - - +
706A SER* 3.8 26.0 - - - +
707A VAL* 4.1 28.5 - - + +
710A PHE* 3.7 36.3 - - + -
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Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 4.7 7.9 - - + -
256A LEU* 5.2 0.2 - - + -
557A GLN 2.8 23.7 + - - +
558A ILE* 3.7 16.2 - - + +
559A LYS 3.3 0.2 - - - -
560A VAL* 1.3 72.8 - - - +
562A SER* 1.3 63.1 - - - +
564A LEU* 3.2 7.2 + - + +
565A PHE* 2.9 49.1 + - + -
710A PHE* 3.9 18.4 - - + -
1T T 3.6 49.1 - - + +
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Residues in contact with SER 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ILE* 5.6 0.2 - - - -
256A LEU* 4.5 17.9 - - - -
260A VAL* 5.2 1.1 - - - -
544A THR 2.8 21.2 + - - -
545A GLY 3.4 7.2 + - - -
546A VAL* 3.9 12.1 - - - -
558A ILE 2.9 17.8 + - - -
559A LYS 3.9 1.1 - - - -
561A VAL* 1.3 78.5 - - - +
563A GLN* 1.3 61.4 + - - +
565A PHE* 4.0 4.4 - - - +
566A ARG* 2.9 46.5 + - - +
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Residues in contact with GLN 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A VAL* 4.2 7.5 - - - +
544A THR* 3.4 39.0 - - - +
559A LYS* 2.9 28.0 + - - +
560A VAL* 3.7 12.6 - - - +
562A SER* 1.3 75.5 - - - +
564A LEU* 1.3 58.3 + - - +
566A ARG* 3.4 7.3 + - - +
567A LYS* 3.0 38.9 + - - +
666A ILE* 3.5 36.9 - - + +
669A GLU* 5.6 2.3 - - - +
670A LEU* 3.6 26.5 - - - +
703A SER* 5.7 1.6 + - - -
707A VAL* 5.1 1.0 - - - +
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Residues in contact with LEU 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 3.9 23.6 - - + -
560A VAL* 2.9 19.5 + - + +
561A VAL* 3.5 7.2 - - - +
563A GLN* 1.3 77.7 - - - +
565A PHE* 1.3 58.6 + - + +
567A LYS* 3.4 2.1 + - - +
568A CYS* 2.8 34.7 + - - +
575A ILE* 4.0 11.7 - - + -
623A CYS* 6.0 0.2 - - - -
624A TYR* 4.1 8.5 - - + -
662A ILE* 4.3 9.4 - - + -
663A LEU* 3.8 26.5 - - + -
666A ILE* 4.0 10.5 - - + +
710A PHE* 4.2 16.8 - - + -
718A LEU* 3.9 28.3 - - + -
1T T 6.3 0.4 - - + -
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Residues in contact with PHE 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ASP* 3.6 41.5 - - + -
251A ASN 3.5 13.7 - - - -
252A ILE* 3.9 23.3 - - + -
257A ARG* 4.1 18.6 + - - -
260A VAL* 4.0 19.5 - - + +
561A VAL* 2.9 42.5 + - + +
562A SER 4.0 3.1 - - - +
564A LEU* 1.3 75.6 - - - +
566A ARG* 1.3 57.9 + - - +
568A CYS* 3.3 3.6 + - - +
569A LEU* 3.0 30.8 + - - +
575A ILE* 3.5 24.5 - - + -
1T T 3.3 27.6 - + + -
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Residues in contact with ARG 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 4.0 7.5 - - - +
259A MET* 3.5 25.1 + - - +
260A VAL* 3.9 26.6 - - + +
263A GLY* 4.3 5.3 - - - -
264A ILE 2.9 34.3 + - - +
265A VAL* 3.9 10.8 - - - +
544A THR 4.7 1.1 - - - -
545A GLY* 2.7 36.9 + - - -
562A SER* 2.9 34.2 + - - +
563A GLN* 3.7 7.4 - - - +
565A PHE* 1.3 78.4 - - - +
567A LYS* 1.3 67.5 + - + +
569A LEU* 3.6 4.9 + - - +
570A GLU* 3.5 23.5 + - - +
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Residues in contact with LYS 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A GLN* 3.0 25.3 + - - +
564A LEU 3.9 0.9 - - - +
566A ARG* 1.3 79.9 - - - +
568A CYS* 1.3 62.9 + - - +
570A GLU* 3.2 41.1 + - - +
571A ILE* 3.4 11.2 - - - +
662A ILE* 3.3 35.1 - - + +
665A ILE* 3.7 24.9 - - + -
666A ILE* 3.8 14.6 - - + +
669A GLU* 3.1 36.9 + - - -
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Residues in contact with CYS 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 3.6 31.9 - - - -
564A LEU* 2.8 25.4 + - - +
565A PHE* 3.8 6.7 - - + +
567A LYS* 1.3 70.0 - - - +
569A LEU* 1.3 66.0 + - - +
571A ILE* 3.0 17.6 + - - +
573A THR* 3.0 51.6 + - - +
575A ILE* 4.1 13.5 - - + -
662A ILE* 4.0 9.2 - - - -
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Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TYR* 5.4 2.2 - - - +
161A TYR* 5.5 2.9 - - - +
199A LYS* 4.6 15.9 - - - +
257A ARG* 4.9 6.3 - - - +
260A VAL* 3.7 27.4 - - + +
261A ASP* 3.7 32.5 - - + +
565A PHE 3.0 16.6 + - - +
566A ARG* 3.7 6.3 - - - +
568A CYS* 1.3 76.9 - - - +
570A GLU* 1.3 63.8 + - + +
571A ILE 3.1 1.2 + - - -
572A ASP* 3.3 14.1 + - - +
573A THR 4.4 2.9 + - - +
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Residues in contact with GLU 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A ARG 3.5 15.4 + - - +
567A LYS* 3.2 32.5 + - - +
569A LEU* 1.3 79.4 - - + +
571A ILE* 1.3 64.2 + - + +
572A ASP* 3.6 2.4 + - - +
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Residues in contact with ILE 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLN* 3.7 13.3 - - - +
210A LYS* 4.7 1.7 - - - +
567A LYS 3.4 13.0 - - - +
568A CYS* 3.0 6.9 + - - +
570A GLU* 1.3 87.2 - - + +
572A ASP* 1.3 73.4 + - - +
573A THR* 3.1 23.9 + - + +
625A THR* 4.8 4.5 - - + -
659A ARG* 6.5 1.1 - - - -
662A ILE* 3.1 37.7 - - + -
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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
------------------------------------------------------------
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