Contacts of the helix formed by residues 614 - 625 (chain D) in PDB entry 5UHG
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 SER 614 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612D TYR* 3.4 5.4 - - - +
613D SER* 1.3 91.1 + - - +
615D PRO* 1.3 78.2 - - - +
616D ALA* 3.1 9.8 + - - +
617D GLU* 2.9 26.4 + - - +
618D ALA* 3.4 4.3 + - - +
635D VAL* 3.9 6.0 - - - +
636D ARG 3.5 4.7 - - - -
638D THR* 6.1 3.4 - - - -
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Residues in contact with PRO 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614D SER* 1.3 88.0 - - - +
616D ALA* 1.3 62.0 + - - +
618D ALA* 3.4 7.4 + - + +
619D ILE* 3.1 35.0 + - + +
635D VAL* 4.0 5.6 - - + -
636D ARG 3.8 11.4 - - - +
637D LEU* 4.0 17.7 - - + -
638D THR* 5.3 10.1 - - + +
668D LEU* 4.5 6.8 - - + +
671D VAL* 4.6 14.1 - - + -
675D GLU* 4.6 16.8 - - - +
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Residues in contact with ALA 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B LEU* 3.7 31.1 - - + +
173B LYS* 4.2 13.5 - - + -
614D SER* 3.1 9.6 - - - +
615D PRO* 1.3 81.2 - - + +
617D GLU* 1.3 61.5 + - - +
619D ILE* 3.6 12.9 - - - +
620D MET* 3.3 27.7 + - - +
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Residues in contact with GLU 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 3.7 22.2 + - - +
146B TYR* 3.4 33.7 + - + -
165B ASP* 3.7 3.5 - - - +
167B ILE* 3.7 20.4 - - + +
612D TYR* 3.6 16.3 - - + -
613D SER* 2.8 35.6 + - - +
614D SER* 2.9 17.1 + - - +
616D ALA* 1.3 76.6 - - - +
618D ALA* 1.3 60.7 + - - +
619D ILE 3.1 1.3 - - - -
620D MET* 2.9 26.6 + - - +
621D ALA* 3.0 10.4 + - - +
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Residues in contact with ALA 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D TYR* 4.1 17.6 - - + -
614D SER 3.4 5.8 + - - +
615D PRO* 3.4 6.8 + - + +
617D GLU* 1.3 78.5 - - - +
619D ILE* 1.3 61.1 + - - +
621D ALA* 3.2 13.9 + - - +
622D ALA 3.3 10.2 + - - -
627D LEU* 3.5 27.7 - - + +
633D ILE* 4.5 4.9 - - + -
635D VAL* 4.9 3.8 - - + -
668D LEU* 3.7 26.1 - - + +
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Residues in contact with ILE 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 3.7 11.9 - - - +
43B LEU* 5.5 2.2 - - + -
173B LYS* 3.3 52.3 - - + +
615D PRO* 3.1 25.7 + - + +
616D ALA* 3.6 8.1 - - - +
617D GLU 3.1 0.4 - - - -
618D ALA* 1.3 74.6 - - - +
620D MET* 1.3 64.4 + - + +
621D ALA 3.0 5.5 + - - -
622D ALA* 3.5 2.5 + - - +
623D ASP* 3.3 25.1 + - - +
668D LEU* 4.5 17.3 - - + -
672D MET* 5.6 13.0 - - + -
675D GLU* 6.1 1.1 - - - +
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Residues in contact with MET 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.9 33.4 - - + +
145B GLY 3.8 12.8 - - - +
146B TYR* 3.7 36.6 - - + +
167B ILE* 4.2 19.3 - - + -
169B SER* 4.0 9.6 - - - -
171B VAL 4.2 8.7 - - - +
172B LEU* 4.0 20.6 - - - +
616D ALA 3.3 13.9 - - - +
617D GLU* 2.9 12.5 + - - +
619D ILE* 1.3 77.8 - - + +
621D ALA* 1.3 58.8 + - - +
622D ALA 3.6 0.2 - - - -
623D ASP* 4.0 8.8 - - - +
624D ARG* 3.5 19.9 + - - +
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Residues in contact with ALA 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B TYR* 4.2 16.6 - - + -
612D TYR* 3.8 23.3 - - + +
617D GLU 3.0 9.5 + - - +
618D ALA 3.3 10.3 - - - +
619D ILE 3.0 0.4 - - - -
620D MET* 1.3 76.3 - - - +
622D ALA* 1.3 60.8 + - - +
623D ASP 3.2 1.3 - - - -
624D ARG* 3.4 2.3 + - - +
625D GLY 3.1 7.1 + - - -
626D VAL* 2.9 29.0 + - + +
627D LEU* 3.6 19.7 - - + +
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Residues in contact with ALA 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D ALA 3.3 10.8 + - - +
619D ILE* 3.5 3.8 + - - +
621D ALA* 1.3 78.6 - - - +
623D ASP* 1.3 64.7 - - - +
624D ARG 3.3 0.2 - - - -
625D GLY* 3.4 11.2 + - - +
626D VAL 4.5 0.2 - - - +
627D LEU* 3.3 29.4 - - + +
629D VAL* 4.7 16.6 - - + -
668D LEU* 4.7 7.2 - - + -
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Residues in contact with ASP 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO 5.1 0.9 - - - +
29A GLY* 4.8 8.1 - - - -
39B ARG* 3.0 39.4 + - - -
40B ARG* 4.0 37.5 + - - +
43B LEU* 4.1 8.2 - - + +
619D ILE* 3.3 18.7 + - - +
620D MET* 4.1 9.2 - - - +
621D ALA 3.2 0.4 - - - -
622D ALA* 1.3 80.7 - - - +
624D ARG* 1.3 61.9 + - - +
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Residues in contact with ARG 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 3.3 32.6 - - - +
29A GLY* 5.7 0.2 - - - -
182A ARG* 2.7 46.6 + - - +
188A ASP* 2.9 30.9 + - - +
144B ARG 5.1 3.0 + - - -
146B TYR* 2.4 36.3 + - + +
147B VAL* 4.1 10.4 - - - +
148B PRO* 3.7 25.6 - - - +
151B GLN* 4.7 5.9 - - - +
620D MET 3.5 11.6 + - - +
621D ALA 3.4 7.5 + - - +
622D ALA 3.3 0.2 - - - -
623D ASP* 1.3 78.1 - - - +
625D GLY* 1.3 58.9 + - - +
626D VAL* 3.9 15.3 - - + -
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Residues in contact with GLY 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596D THR* 4.8 4.0 + - - -
621D ALA 3.1 2.8 + - - -
622D ALA* 3.4 11.9 + - - -
623D ASP 3.4 1.8 - - - -
624D ARG* 1.3 81.4 - - - +
626D VAL* 1.3 65.1 + - - +
627D LEU 3.7 3.1 - - - -
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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