Contacts of the strand formed by residues 94 - 102 (chain K) in PDB entry 3Q3G
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 94 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40K LYS* 3.7 33.4 - - + -
41K GLN 3.5 16.4 - - - +
42K ARG* 3.9 4.7 - - - +
43K PRO* 4.6 5.2 - - - -
92K ASP 3.2 2.4 + - - -
93K THR* 1.4 76.7 - - - +
95K VAL* 1.3 63.6 + - - +
96K TYR* 3.6 15.2 - - + -
119K THR* 3.8 2.5 - - - +
120K VAL 3.0 29.7 + - - +
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Residues in contact with VAL 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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39K VAL 3.9 0.5 - - - +
40K LYS* 3.7 1.2 - - - -
41K GLN* 2.8 42.6 + - + +
94K ALA* 1.3 75.3 - - - +
96K TYR* 1.3 61.4 + - - +
97K TYR* 3.6 40.2 + - + +
116K GLN 5.2 0.4 - - - +
117K GLY* 4.0 13.2 - - - -
118K THR 3.4 6.3 - - - +
119K THR* 4.0 23.6 - - + +
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Residues in contact with TYR 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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8K GLN* 2.8 26.1 + - - -
22K LEU* 3.7 20.9 - - + -
38K TRP* 4.5 3.1 - - + -
39K VAL 3.5 2.0 - - - +
40K LYS* 3.6 33.9 + - + -
50K ILE* 3.6 28.7 - - + -
66K PHE* 5.6 1.4 - + - -
83K LEU* 3.8 11.4 - - + -
85K LEU* 3.6 21.1 - - + +
92K ASP* 2.6 44.8 + - - +
94K ALA* 3.6 14.8 - - + -
95K VAL* 1.3 71.9 - - - +
97K TYR* 1.3 56.9 + - - +
117K GLY* 3.4 0.2 - - - -
118K THR 2.9 20.2 + - - +
120K VAL* 3.6 28.9 - - + -
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Residues in contact with TYR 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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44J GLN* 3.4 6.8 + - - -
48J GLN 3.8 9.0 + - - -
49J SER* 3.4 22.6 - - - -
50J PRO* 4.0 14.4 - - + -
8K GLN* 3.6 1.6 - - - -
38K TRP* 3.4 9.6 - - - -
39K VAL* 2.8 40.7 + - - +
41K GLN* 3.3 39.3 + - + -
47K LEU* 4.5 4.3 - - + -
95K VAL* 3.6 23.4 - - + +
96K TYR* 1.3 75.2 - - - +
98K CYS* 1.3 62.0 + - - +
114K TRP* 3.8 27.4 - + + -
115K GLY 3.5 17.5 - - - -
116K GLN 3.7 4.7 + - - -
117K GLY* 3.6 19.5 - - - -
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Residues in contact with CYS 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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6K LEU* 3.7 11.8 - - - +
8K GLN* 3.2 25.2 + - - -
24K CYS* 2.0 53.8 - - + -
36K MET* 4.6 4.7 - - + -
37K GLN 3.3 11.9 - - - +
38K TRP* 3.9 13.5 - - + -
97K TYR* 1.3 76.6 - - - +
99K ALA* 1.3 59.9 + - - +
114K TRP* 3.5 1.4 - - - -
115K GLY 2.8 26.3 + - - -
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Residues in contact with ALA 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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6K LEU* 3.9 4.0 - - - -
36K MET* 3.6 5.4 - - - +
37K GLN* 2.7 37.5 + - + +
39K VAL* 5.0 2.0 - - + -
97K TYR 4.1 0.2 - - - -
98K CYS* 1.3 75.8 - - - +
100K SER* 1.3 57.2 + - - +
111K MET* 3.8 31.4 - - + -
113K TYR 3.1 13.7 - - - +
114K TRP* 3.9 20.2 - - + -
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Residues in contact with SER 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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6K LEU* 3.9 1.7 - - - +
29K PHE* 4.0 11.5 - - - -
34K ILE* 3.8 36.3 - - - +
35K TYR 3.4 4.0 - - - -
36K MET* 4.3 4.5 - - - -
37K GLN* 4.6 0.7 - - - -
99K ALA* 1.3 75.5 - - - +
101K GLU* 1.3 58.5 + - - +
102K GLY* 4.9 0.2 - - - -
111K MET* 3.2 6.1 - - - -
112K ASP* 3.1 28.1 + - - +
113K TYR* 2.9 33.6 + - - +
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Residues in contact with GLU 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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97J TYR* 5.0 0.3 - - - +
100J TYR* 4.6 1.7 + - - -
102J LEU* 4.4 11.1 - - - +
34K ILE* 3.7 2.8 - - - +
35K TYR* 2.9 47.5 + - + +
37K GLN* 3.7 24.6 + - + +
100K SER* 1.3 71.4 - - - +
102K GLY* 1.3 62.1 + - - +
103K HIS* 4.3 3.1 + - - -
108K GLY* 3.6 3.3 - - - -
109K TYR* 3.2 37.3 + - + +
110K ALA 3.4 14.1 - - - +
111K MET* 4.8 2.6 - - + +
208L ARG* 2.8 40.2 + - - -
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Residues in contact with GLY 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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34K ILE* 3.8 16.6 - - - +
100K SER 3.9 0.8 - - - -
101K GLU* 1.3 77.9 - - - +
103K HIS* 1.3 66.3 + - - -
104K TYR* 3.6 25.7 + - - -
108K GLY 4.9 0.9 - - - -
109K TYR* 3.3 22.3 - - - +
110K ALA 4.2 1.4 + - - -
112K ASP* 3.3 13.2 + - - -
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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