Contacts of the helix formed by residues 925 - 937 (chain D) in PDB entry 6GHM
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 925 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A MET* 4.5 9.8 - - + +
291A CYS 2.9 17.1 + - - +
292A SER* 4.0 18.5 - - - -
924D PHE* 1.3 72.4 - - - +
926D PRO* 1.3 80.5 - - - +
927D LEU* 3.5 21.3 + - - +
928D ALA* 2.9 42.6 + - + +
929D LEU* 2.9 10.0 + - - +
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Residues in contact with PRO 926 (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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290A MET* 4.2 19.7 - - + -
924D PHE 3.6 7.9 - - - +
925D ASN* 1.3 89.8 - - - +
927D LEU* 1.3 57.0 + - - +
929D LEU* 3.0 5.0 + - + +
930D LEU* 2.8 29.3 + - - +
945D ILE* 3.7 26.5 - - + +
948D GLU* 3.8 30.5 - - + +
949D VAL* 3.8 11.2 - - + -
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Residues in contact with LEU 927 (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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925D ASN* 3.2 18.1 + - - +
926D PRO* 1.3 78.4 - - - +
928D ALA* 1.3 64.7 + - - +
930D LEU* 3.2 16.1 + - + -
931D LEU* 3.0 48.7 + - + +
949D VAL* 3.9 12.6 - - + +
951D ASP 4.7 11.2 - - - +
952D PRO 5.3 0.9 - - - +
954D LEU* 3.8 27.4 - - + +
955D PRO 4.4 13.2 - - - +
956D ASN* 5.2 1.8 - - - -
962D ALA* 6.2 0.2 - - + -
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Residues in contact with ALA 928 (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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255A TYR* 4.5 16.4 + - - +
257A PHE* 5.0 6.5 - - + -
293A PHE* 4.9 14.4 - - + +
924D PHE* 5.0 5.2 - - + -
925D ASN* 2.9 31.9 + - + +
927D LEU* 1.3 81.8 - - - +
929D LEU* 1.3 56.8 + - - +
931D LEU* 3.7 7.7 + - - +
932D ASP* 3.1 29.5 + - - +
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Residues in contact with LEU 929 (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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257A PHE* 5.6 0.9 - - + -
261A ARG* 3.6 38.6 - - - +
923D LYS* 5.9 2.0 - - + -
924D PHE* 3.7 42.2 - - + +
925D ASN 2.9 6.1 + - - +
926D PRO 3.0 8.9 + - - +
928D ALA* 1.3 77.0 - - - +
930D LEU* 1.3 53.2 + - - +
932D ASP* 4.6 1.1 - - + +
933D SER* 2.5 41.4 + - - -
941D LEU* 4.0 17.2 - - + +
945D ILE* 3.7 28.0 - - + -
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Residues in contact with LEU 930 (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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926D PRO 2.8 15.9 + - - +
927D LEU* 3.2 15.0 + - + +
929D LEU* 1.3 73.6 - - - +
931D LEU* 1.3 60.5 + - - +
933D SER* 3.3 3.1 + - - +
934D SER* 2.9 43.1 + - - +
942D VAL* 4.0 20.6 - - + -
945D ILE* 4.0 17.4 - - + +
946D ILE* 4.5 10.1 - - + -
949D VAL* 4.2 15.0 - - + -
952D PRO* 3.9 34.8 - - + +
962D ALA* 3.7 20.4 - - + +
978D LEU* 4.5 6.7 - - + -
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Residues in contact with LEU 931 (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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255A TYR* 5.9 2.9 - - - +
407A GOL 5.2 2.5 - - - +
927D LEU* 3.0 44.1 + - + +
928D ALA* 4.0 7.2 - - - +
930D LEU* 1.3 78.4 - - - +
932D ASP* 1.3 57.8 + - - +
934D SER* 3.5 1.0 + - - -
935D LEU* 3.0 23.0 + - - +
954D LEU 5.0 4.0 - - - +
956D ASN* 3.9 27.6 - - + +
960D ILE* 3.8 10.3 - - + +
961D THR* 3.4 9.9 - - - -
962D ALA* 3.3 31.6 - - + +
965D ASN* 3.0 26.4 + - - +
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Residues in contact with ASP 932 (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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257A PHE* 3.6 31.5 - - + +
261A ARG* 2.9 29.3 + - - +
407A GOL 2.9 35.0 + - - +
928D ALA 3.1 16.8 + - - +
929D LEU* 4.2 3.1 - - - +
931D LEU* 1.3 80.9 - - - +
933D SER* 1.3 57.4 + - - +
935D LEU* 3.1 3.9 + - - +
936D GLU* 2.8 47.9 + - - +
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Residues in contact with SER 933 (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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261A ARG* 4.5 3.5 - - - +
929D LEU 2.5 25.7 + - - -
930D LEU* 3.3 5.5 + - - -
932D ASP* 1.3 75.7 + - - +
934D SER* 1.3 59.5 + - - +
936D GLU* 4.4 2.9 - - - +
937D GLY* 2.9 24.1 + - - -
938D GLU* 3.0 23.8 + - - -
941D LEU* 3.7 26.5 - - - +
942D VAL* 3.3 26.7 + - - +
945D ILE* 4.4 0.3 - - - +
974D ILE* 4.0 0.2 - - - +
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Residues in contact with SER 934 (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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930D LEU* 2.9 26.2 + - - +
931D LEU 3.8 2.9 - - - -
933D SER* 1.3 78.4 + - - +
935D LEU* 1.3 61.5 + - - +
937D GLY 3.9 0.2 + - - -
942D VAL* 3.8 15.6 - - - +
962D ALA* 3.5 33.3 - - - +
965D ASN* 4.2 1.8 - - - -
966D ALA* 3.5 13.2 - - - +
971D HIS* 3.4 17.8 - - - -
974D ILE* 4.0 12.1 - - - +
978D LEU* 3.8 9.9 - - - +
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Residues in contact with LEU 935 (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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407A GOL 3.7 31.0 - - - +
931D LEU 3.0 17.7 + - - +
932D ASP* 3.1 4.7 + - - +
934D SER* 1.3 78.8 - - - +
936D GLU* 1.3 71.9 + - - +
965D ASN* 3.6 32.3 - - + +
968D CYS* 5.8 2.9 - - + -
969D ALA* 3.3 22.9 - - + +
971D HIS* 3.2 14.9 + - - -
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Residues in contact with GLU 936 (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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407A GOL 5.6 0.7 - - - -
1045C GLN* 4.7 3.3 + - - -
932D ASP* 2.8 36.1 + - - +
933D SER 4.3 1.8 - - - +
935D LEU* 1.3 97.0 - - + +
937D GLY* 1.3 62.0 + - - +
938D GLU* 3.5 22.9 + - + +
971D HIS* 3.5 8.0 + - - -
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Residues in contact with GLY 937 (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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1041C THR* 3.4 9.3 - - - +
1045C GLN* 3.2 23.3 + - - +
933D SER 2.9 6.3 + - - -
935D LEU 3.4 0.6 - - - -
936D GLU* 1.3 78.6 - - - +
938D GLU* 1.3 59.6 + - - +
939D PHE 3.0 8.0 + - - -
971D HIS* 3.3 33.6 + - - -
974D ILE* 3.7 6.3 - - - -
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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