Contacts of the helix formed by residues 546 - 563 (chain A) in PDB entry 3L4U
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 THR 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A THR* 2.8 28.9 + - + -
545A ALA* 1.3 79.3 - - - +
547A TRP* 1.3 65.6 + - - +
548A ASP* 3.3 10.9 + - - +
549A ASP* 2.7 30.7 + - - +
550A LEU* 3.2 16.8 + - - +
577A LEU* 4.6 5.2 - - + -
583A LEU* 3.6 12.0 - - - +
587A TRP* 4.0 1.0 - - - -
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Residues in contact with TRP 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A THR* 1.3 75.1 - - - +
548A ASP* 1.3 62.7 + - - +
550A LEU* 3.3 29.1 + - + +
551A ARG* 3.1 43.4 + - - +
580A PRO* 5.3 6.5 - - + +
582A GLU* 3.8 20.6 - - + -
583A LEU* 3.5 40.6 - - + +
586A ARG* 3.6 28.9 - - + -
684A LEU* 3.5 14.1 - - - +
685A ASP 3.6 17.3 - - - -
686A GLU* 3.5 55.8 - - + +
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Residues in contact with ASP 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A THR* 3.2 9.9 + - - +
547A TRP* 1.3 76.9 - - - +
549A ASP* 1.3 57.5 + - - +
551A ARG* 2.8 35.2 + - - +
552A TRP* 2.9 71.8 + - + +
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Residues in contact with ASP 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PRO 3.8 14.2 - - - +
207A ASN* 5.6 0.2 - - - -
543A ASN* 3.5 13.7 + - + +
544A THR* 3.1 51.1 + - - +
546A THR* 2.7 27.3 + - - +
548A ASP* 1.3 76.5 - - - +
550A LEU* 1.3 64.7 + - - +
552A TRP* 3.3 21.7 + - - +
553A SER* 3.2 22.3 + - - -
587A TRP* 3.8 11.8 - - + -
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Residues in contact with LEU 550 (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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546A THR 3.2 13.0 + - - +
547A TRP* 3.4 42.0 - - + +
549A ASP* 1.3 75.0 - - - +
551A ARG* 1.3 61.1 + - - +
553A SER* 2.8 24.6 + - - -
554A ILE* 4.3 1.4 + - - +
583A LEU* 3.7 13.5 - - + -
586A ARG* 4.4 8.1 - - + +
587A TRP* 3.6 49.3 - - + +
590A LEU* 3.9 20.9 - - + +
683A VAL 4.3 4.0 - - - +
684A LEU* 3.8 22.5 - - + +
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Residues in contact with ARG 551 (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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186A GLN 5.3 1.4 - - - +
547A TRP* 3.1 23.5 + - - +
548A ASP* 2.8 43.5 + - - +
550A LEU* 1.3 78.7 - - - +
552A TRP* 1.3 68.4 + - + +
553A SER 3.2 1.0 + - - -
554A ILE* 3.5 13.6 + - - +
555A PRO* 3.5 10.7 - - - +
669A HIS* 4.9 7.0 + - + +
670A GLN* 6.5 1.1 - - - -
684A LEU* 2.9 59.5 + - + +
685A ASP* 3.4 20.8 + - - +
686A GLU 5.0 0.4 - - - +
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Residues in contact with TRP 552 (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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184A VAL* 3.8 30.6 - - + +
186A GLN* 3.5 53.0 + - + +
206A PRO 4.7 2.9 - - - -
207A ASN* 3.8 8.7 - - - -
208A GLY* 3.6 31.2 - - - -
540A LEU* 5.5 0.2 - - - +
548A ASP* 2.9 61.5 + - + +
549A ASP* 3.3 22.4 + - - +
551A ARG* 1.3 78.9 - - + +
553A SER* 1.3 62.6 + - - +
554A ILE 3.3 0.8 + - - -
555A PRO* 3.6 15.1 - - - +
556A GLY* 3.6 9.2 + - - -
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Residues in contact with SER 553 (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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540A LEU* 3.9 8.4 - - - +
549A ASP 3.2 10.2 + - - -
550A LEU* 2.8 18.4 + - - -
551A ARG 3.1 0.2 - - - -
552A TRP* 1.3 76.7 - - - +
554A ILE* 1.3 68.6 + - - +
556A GLY* 3.3 1.2 + - - -
557A VAL* 3.0 28.0 + - - +
570A PRO* 3.8 24.5 - - - -
587A TRP* 4.9 0.9 - - - -
590A LEU* 4.4 0.2 - - - +
594A TYR* 2.6 31.8 + - - -
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Residues in contact with ILE 554 (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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550A LEU 4.9 0.7 - - - +
551A ARG 3.5 5.3 + - - +
552A TRP 3.3 0.2 - - - -
553A SER* 1.3 81.1 + - - +
555A PRO* 1.4 74.4 - - + +
557A VAL* 3.2 8.1 + - + +
558A LEU* 3.0 35.7 + - + +
590A LEU* 4.1 14.8 - - + -
594A TYR* 4.9 3.4 - - + -
669A HIS 3.3 23.6 - - - +
670A GLN 4.0 11.9 - - - +
671A GLN 4.4 2.7 - - - +
672A PHE* 4.0 29.4 - - + -
682A PRO* 3.9 27.4 - - + -
684A LEU* 4.1 11.7 - - + -
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Residues in contact with PRO 555 (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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185A HIS* 5.4 1.6 - - + +
186A GLN 4.0 13.5 - - - +
187A GLN 3.7 35.2 - - - +
188A TYR* 3.9 12.8 - - + +
551A ARG 3.5 13.2 - - - +
552A TRP 3.6 7.6 - - - +
554A ILE* 1.4 92.5 - - + +
556A GLY* 1.3 55.7 + - - +
558A LEU* 3.3 3.8 + - + +
559A GLU* 2.8 44.9 + - - +
669A HIS* 3.9 22.2 - - + +
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Residues in contact with GLY 556 (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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183A HIS 5.3 5.2 - - - -
540A LEU* 4.1 19.5 - - - -
552A TRP 3.6 7.6 + - - -
553A SER 3.3 5.7 + - - -
554A ILE 3.2 1.2 - - - -
555A PRO* 1.3 79.9 - - - +
557A VAL* 1.3 60.9 + - - +
559A GLU* 3.8 11.5 - - - +
560A PHE* 3.1 32.3 + - - -
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Residues in contact with VAL 557 (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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540A LEU* 4.1 6.5 - - + +
553A SER 3.0 20.3 + - - +
554A ILE* 3.6 6.1 - - + +
556A GLY* 1.3 73.9 - - - +
558A LEU* 1.3 68.8 + - + +
560A PHE 3.4 1.0 + - - -
561A ASN* 3.0 31.4 + - - +
568A VAL* 3.7 22.0 - - + +
569A GLY* 4.1 9.9 - - - -
570A PRO* 4.4 0.4 - - + -
594A TYR* 3.9 26.5 - - + -
595A PRO* 3.8 15.7 - - + -
652A ALA* 3.7 25.8 - - + -
672A PHE* 5.4 5.4 - - + -
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Residues in contact with LEU 558 (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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188A TYR* 3.7 43.4 + - + +
554A ILE* 3.0 35.7 + - + +
555A PRO* 3.7 2.5 - - + +
557A VAL* 1.3 75.9 - - + +
559A GLU* 1.3 63.8 + - - +
561A ASN* 3.2 8.2 + - - +
562A LEU* 3.1 23.2 + - - +
652A ALA* 3.7 26.9 - - + +
653A ARG 3.8 18.8 - - - -
654A PRO* 3.8 14.7 - - + +
668A VAL 5.1 1.1 - - - +
669A HIS* 5.0 5.2 - - - -
671A GLN 5.0 3.8 - - - +
672A PHE* 4.0 15.0 - - + -
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Residues in contact with GLU 559 (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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179A GLY* 4.5 13.3 + - - +
180A LEU 4.4 1.6 - - - +
183A HIS 4.1 10.2 + - - +
185A HIS* 2.6 44.8 + - - +
187A GLN 4.0 7.6 - - - +
188A TYR* 3.7 22.1 - - + +
555A PRO* 2.8 27.0 + - - +
556A GLY* 3.8 11.8 - - - +
558A LEU* 1.3 76.2 - - - +
560A PHE* 1.3 65.1 + - + +
562A LEU* 3.0 22.4 + - - +
563A PHE* 3.1 33.0 + - + -
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Residues in contact with PHE 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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182A GLU* 3.5 40.2 - - + -
183A HIS 6.1 0.2 - - - -
217A GLN* 4.4 3.1 - - + -
528A THR* 3.9 13.2 - - - -
538A HIS* 3.4 30.7 - + - -
540A LEU* 3.8 11.7 - - + -
556A GLY* 3.1 31.2 + - - +
558A LEU 3.4 0.2 - - - -
559A GLU* 1.3 78.5 - - + +
561A ASN* 1.3 59.4 + - - +
563A PHE* 3.2 30.5 + + - +
564A GLY 3.2 0.2 + - - -
565A ILE* 2.8 71.0 + - + +
568A VAL* 3.8 12.3 - - + -
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Residues in contact with ASN 561 (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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274A VAL* 4.3 3.6 - - - +
278A LEU* 5.0 1.0 - - - +
557A VAL 3.0 25.0 + - - +
558A LEU 3.5 7.0 - - - +
559A GLU 3.2 0.8 - - - -
560A PHE* 1.3 74.8 - - - +
562A LEU* 1.3 63.7 + - - +
564A GLY* 3.1 13.9 + - - -
566A PRO* 3.4 37.1 + - - +
568A VAL* 3.5 8.7 - - - +
649A ASP 5.5 0.2 - - - +
650A THR* 3.9 19.7 - - + +
651A VAL* 2.9 26.3 + - - +
652A ALA* 2.9 37.7 + - - +
654A PRO* 6.4 0.2 - - + -
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Residues in contact with LEU 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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178A TYR* 3.9 31.4 - - + +
179A GLY* 4.0 9.6 - - - +
188A TYR* 3.3 31.2 - - + +
219A PHE* 4.0 13.2 - - + -
221A LEU* 4.3 11.2 - - + -
274A VAL* 3.7 26.6 - - + +
277A TYR* 3.6 18.0 - - - -
278A LEU* 4.3 0.2 - - - +
558A LEU 3.1 13.4 + - - +
559A GLU* 3.0 9.5 + - - +
561A ASN* 1.3 76.7 - - - +
563A PHE* 1.3 60.5 + - + +
564A GLY 3.1 3.3 + - - -
650A THR* 4.6 3.8 - - + -
654A PRO* 5.2 1.6 - - + -
657A HIS* 3.6 28.3 - - + +
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Residues in contact with PHE 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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179A GLY* 4.0 9.2 - - - -
180A LEU 3.3 34.8 - - - -
181A GLY* 4.4 3.8 - - - -
217A GLN* 3.6 48.7 - - + +
219A PHE* 3.5 37.2 - + + -
277A TYR* 4.0 10.7 + + - -
278A LEU* 4.0 9.4 - - - +
281A ILE* 4.5 5.5 - - - +
531A GLY* 4.8 5.5 + - - -
533A GLY 5.4 0.2 + - - -
559A GLU* 3.1 29.0 + - + -
560A PHE* 3.6 31.6 - + + +
561A ASN 3.2 0.8 - - - -
562A LEU* 1.3 79.8 - - + +
564A GLY* 1.3 61.3 + - - +
565A ILE* 3.3 7.7 + - + +
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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