Contacts of the helix formed by residues 92 - 102 (chain K) in PDB entry 6D6Q
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 GLN 92 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91K LEU* 1.3 75.6 - - - +
93K THR* 1.3 61.7 + - - +
94K VAL 3.3 0.2 - - - -
95K LEU* 3.2 7.1 + - + +
96K GLN* 2.9 33.9 + - + +
122K THR* 5.2 3.6 - - + -
123K PHE 3.3 11.1 + - - +
124K THR* 3.4 16.2 - - + +
125K ASN* 3.4 14.6 + - - +
126K GLU* 3.0 40.3 + - + +
127K HIS* 3.6 26.1 + - - -
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Residues in contact with THR 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K LEU* 4.5 0.9 - - - +
92K GLN* 1.3 71.7 - - - +
94K VAL* 1.3 74.9 + - - +
96K GLN* 3.2 11.9 + - - +
97K GLU* 2.9 31.0 + - - +
125K ASN* 3.5 18.8 + - - +
126K GLU* 2.9 32.1 - - + +
145K ASN* 3.5 28.2 - - - +
148K ALA* 4.6 6.7 - - + -
149K ILE* 3.5 26.7 - - - +
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Residues in contact with VAL 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K PRO* 3.9 17.9 - - + +
69K ASP 4.2 0.4 - - - -
70K THR* 3.9 26.4 + - - +
73K LEU* 3.9 34.8 - - + -
90K VAL* 5.3 6.3 - - + -
91K LEU* 4.0 23.6 - - + +
93K THR* 1.3 83.4 + - - +
95K LEU* 1.3 58.1 + - - +
97K GLU* 3.3 2.4 + - - +
98K VAL* 2.9 33.1 + - + +
149K ILE* 3.8 26.4 - - + +
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Residues in contact with LEU 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 5.2 5.8 - - - +
90K VAL* 4.7 7.2 - - + -
91K LEU 3.6 16.3 + - - +
92K GLN* 3.2 10.4 + - + +
93K THR 3.2 0.8 - - - -
94K VAL* 1.3 81.1 - - - +
96K GLN* 1.3 57.8 + - - +
98K VAL* 3.4 9.6 + - + +
99K ARG* 2.9 28.6 + - - +
106K TYR* 3.4 38.1 - - + +
109K ILE* 4.2 26.9 - - + -
110K ARG* 4.9 7.6 - - + -
113K THR* 6.4 1.8 - - + -
122K THR* 4.8 16.4 - - + +
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Residues in contact with GLN 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU 5.8 6.0 - - - +
92K GLN* 2.9 22.6 + - + +
93K THR* 3.2 14.6 + - - +
95K LEU* 1.3 77.4 - - - +
97K GLU* 1.3 58.9 + - + +
99K ARG* 3.2 12.7 + - + +
100K ASN* 2.9 47.2 + - - +
106K TYR* 5.6 0.2 - - - -
126K GLU* 5.3 5.7 - - - +
145K ASN* 5.5 2.1 - - - +
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Residues in contact with GLU 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K THR* 2.2 44.5 + - + +
93K THR 2.9 19.5 + - - +
94K VAL 3.7 3.4 - - - +
96K GLN* 1.3 74.8 - - + +
98K VAL* 1.3 67.0 + - - +
100K ASN* 3.0 10.5 + - - +
101K ARG* 2.9 48.5 + - - +
142K ASN* 4.4 11.6 - - - +
145K ASN* 2.6 42.3 + - - +
149K ILE* 5.7 1.9 - - - +
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Residues in contact with VAL 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K THR* 4.6 5.1 - - + +
73K LEU* 3.7 31.0 - - + -
74K LEU* 4.4 17.3 - - + -
94K VAL* 2.9 25.2 + - + +
95K LEU* 3.6 9.9 - - + +
97K GLU* 1.3 74.5 - - - +
99K ARG* 1.3 56.7 + - - +
102K SER 2.6 36.7 + - - +
105K VAL* 3.6 17.9 - - + +
106K TYR* 3.4 33.9 - - + +
109K ILE* 4.9 4.3 - - + -
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Residues in contact with ARG 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 2.5 49.6 + - - +
4B GLU* 4.4 9.4 + - - +
95K LEU 2.9 15.3 + - - +
96K GLN* 3.3 16.2 - - - +
98K VAL* 1.3 79.2 - - - +
100K ASN* 1.3 71.1 + - - +
101K ARG 3.5 0.2 + - - -
102K SER 3.8 8.1 - - - +
103K ALA* 4.6 3.8 + - - +
106K TYR* 3.5 52.5 + - + -
365K ILE* 4.2 28.9 - - + +
367K GLU* 4.4 13.1 + - - +
47O C 5.3 6.4 + - - +
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Residues in contact with ASN 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU 5.0 3.6 + - - -
96K GLN* 2.9 42.7 + - - +
97K GLU* 3.0 10.3 + - - +
99K ARG* 1.3 91.9 + - - +
101K ARG* 1.3 71.1 + - - +
47O C 3.6 25.9 - - - +
48O A 5.7 0.3 - - - -
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Residues in contact with ARG 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K THR* 3.9 25.5 - - - +
71K ASN* 5.6 1.0 + - - -
74K LEU* 4.0 24.1 - - + +
97K GLU* 2.9 44.1 + - - +
98K VAL 4.3 0.7 - - - +
99K ARG 4.4 0.2 - - - -
100K ASN* 1.3 87.7 - - - +
102K SER* 1.3 61.1 + - - +
142K ASN* 5.4 10.5 - - - +
48O A 3.9 23.7 + - - +
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Residues in contact with SER 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74K LEU* 4.6 9.4 - - - -
98K VAL 2.6 22.9 + - - +
99K ARG 3.8 4.3 - - - +
101K ARG* 1.3 78.9 - - - +
103K ALA* 1.3 60.7 + - - +
104K PRO* 3.3 16.0 - - - +
105K VAL* 3.2 33.5 - - - +
106K TYR* 3.6 12.3 + - - +
48O A 4.9 3.4 - - - -
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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