Contacts of the helix formed by residues 994 - 1005 (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 ALA 994 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077C GLN 3.4 26.4 + - - +
1078C ALA* 4.6 3.9 + - - -
1080C GLY* 5.9 1.2 - - - -
884D VAL 4.2 0.7 - - - -
885D ILE* 3.7 26.0 - - + -
992D GLY 3.5 2.8 + - - -
993D GLU* 1.3 70.4 - - - +
995D VAL* 1.3 56.9 + - - +
996D GLY 2.8 12.3 + - - -
997D ILE* 3.2 26.0 + - + -
998D VAL* 3.3 14.5 + - - +
1248D LEU* 4.7 1.6 - - + -
1260D ALA* 4.5 6.7 - - + -
51E TYR* 4.6 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 995 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884D VAL* 4.1 19.5 - - + +
886D VAL* 3.7 26.0 - - + +
974D VAL* 4.7 5.6 - - + -
979D TYR* 3.5 48.1 + - + +
989D VAL* 4.1 8.7 - - + -
993D GLU* 2.8 28.7 + - + +
994D ALA* 1.3 70.2 - - - +
996D GLY* 1.3 62.4 + - - +
998D VAL* 4.0 11.2 - - + +
999D ALA* 3.1 22.7 + - - +
1156D VAL* 4.4 6.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 996 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881D SER* 3.4 36.8 + - - -
884D VAL* 3.6 9.1 + - - -
994D ALA 2.8 3.6 + - - -
995D VAL* 1.3 79.9 - - - +
997D ILE* 1.3 63.6 + - - -
999D ALA* 3.0 6.6 + - - +
1000D ALA* 3.0 18.0 + - - +
1156D VAL* 4.0 11.9 - - - -
1157D ILE* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 997 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074C TRP* 3.9 18.4 - - + +
1077C GLN* 3.2 43.5 - - + +
1078C ALA* 4.7 2.7 - - + -
878D VAL* 4.2 18.8 - - + +
881D SER* 4.2 11.7 - - - +
882D GLN* 4.5 9.0 - - + -
994D ALA* 3.2 13.9 + - + +
996D GLY* 1.3 74.1 - - - +
998D VAL* 1.3 58.7 + - - +
1000D ALA* 3.0 7.6 + - - +
1001D GLN* 2.8 49.9 + - - +
1248D LEU* 3.5 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 998 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078C ALA* 3.7 30.7 - - + +
506D ARG* 4.5 13.7 - - + +
568D PRO* 3.8 29.4 - - + -
979D TYR* 5.2 2.9 - - - +
993D GLU* 5.0 6.5 - - + +
994D ALA 3.3 20.9 - - - +
995D VAL* 4.0 8.3 - - - +
997D ILE* 1.3 75.7 - - - +
999D ALA* 1.3 54.1 + - - +
1001D GLN* 3.5 10.9 + - - +
1002D SER* 2.5 39.1 + - - +
1153D HIS* 4.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 999 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995D VAL 3.1 18.9 + - - +
996D GLY 3.0 7.0 + - - +
998D VAL* 1.3 74.9 - - - +
1000D ALA* 1.3 64.9 + - - +
1002D SER* 3.1 3.1 + - - -
1003D ILE* 3.0 30.1 + - - +
1153D HIS* 3.4 46.8 + - + +
1156D VAL* 4.2 9.9 - - + -
1157D ILE* 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1000 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874D THR* 4.3 5.5 - - - +
877D LEU* 3.6 49.6 - - + +
878D VAL* 3.8 15.7 - - + -
881D SER* 4.6 0.4 - - - +
996D GLY 3.0 11.1 + - - +
997D ILE 3.4 7.9 - - - +
999D ALA* 1.3 76.4 - - - +
1001D GLN* 1.3 62.9 + - - +
1003D ILE* 3.2 4.4 + - - +
1004D GLY* 3.0 20.3 + - - -
1157D ILE* 4.5 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1001 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071C MET 5.0 1.0 + - - -
1074C TRP* 3.2 47.1 + - + +
1075C ALA* 3.5 7.1 - - - +
1078C ALA* 3.5 8.7 - - - +
503D THR 5.8 1.0 + - - -
504D LEU 3.6 18.6 - - - +
505D HIS* 3.8 11.4 - - + +
506D ARG* 2.9 32.7 + - - +
874D THR* 4.8 7.0 - - + -
878D VAL* 5.3 4.0 - - + -
997D ILE* 2.8 22.6 + - + +
998D VAL* 3.7 8.4 - - - +
1000D ALA* 1.3 76.0 - - + +
1002D SER* 1.3 58.3 + - - +
1005D GLU* 2.9 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1002 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D HIS* 5.2 2.2 - - - +
568D PRO* 4.1 3.3 + - - +
569D ALA* 3.6 39.7 + - - +
998D VAL* 2.5 26.0 + - - +
999D ALA 3.1 7.6 + - - -
1001D GLN* 1.3 75.9 - - - +
1003D ILE* 1.3 60.4 + - - +
1005D GLU* 4.5 3.0 - - - +
1006D PRO* 3.3 17.0 - - - +
1149D ILE* 3.6 13.6 - - - +
1153D HIS* 4.0 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1003 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873D LEU* 5.4 1.8 - - + -
877D LEU* 4.1 15.9 - - + -
999D ALA 3.0 16.6 + - - +
1000D ALA 3.7 4.9 - - - +
1002D SER* 1.3 78.7 - - - +
1004D GLY* 1.3 60.3 + - - +
1006D PRO* 3.2 13.7 - - - +
1007D GLY 4.2 0.9 + - - -
1031D VAL* 4.9 0.9 - - + -
1035D PHE* 3.8 27.1 - - + -
1142D TYR* 3.1 46.1 + - + +
1149D ILE* 3.8 6.7 - - + -
1153D HIS* 4.2 6.5 - - + +
1154D ILE* 3.8 32.5 - - + -
1157D ILE* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1004 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504D LEU* 5.5 3.0 - - - +
870D SER* 3.1 17.5 + - - -
873D LEU* 5.2 5.6 - - - -
874D THR* 3.6 24.0 + - - -
877D LEU* 4.6 4.9 - - - +
1000D ALA 3.0 13.0 + - - -
1001D GLN 4.0 0.2 - - - -
1003D ILE* 1.3 78.6 - - - +
1005D GLU* 1.3 61.2 + - - +
1006D PRO 3.4 0.2 - - - -
1007D GLY* 2.9 17.8 + - - -
1008D THR* 5.5 0.2 + - - -
1142D TYR* 5.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1005 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504D LEU* 4.0 41.8 + - + +
505D HIS* 3.3 39.0 + - + +
569D ALA* 5.2 6.9 - - - +
874D THR* 5.5 0.2 - - - +
1001D GLN 2.9 17.6 + - - +
1002D SER* 4.5 3.4 - - - +
1004D GLY* 1.3 75.6 - - - +
1006D PRO* 1.3 83.1 - - + +
1007D GLY 3.3 0.9 + - - -
1008D THR* 4.4 6.4 + - - -
1009D GLN* 5.3 2.9 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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