Contacts of the strand formed by residues 7 - 17 (chain K) in PDB entry 3MQT
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 ILE 7 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6K ASN* 1.3 73.3 - - - +
8K VAL* 1.3 63.2 - - - +
9K SER 3.8 11.7 - - - +
10K VAL* 4.5 2.7 - - + -
31K VAL* 3.5 25.8 - - + -
32K THR 3.7 4.0 - - - +
33K ASP* 4.1 1.3 - - - +
70K VAL* 3.6 33.2 - - + +
71K ILE* 3.6 11.8 - - + +
72K GLY* 2.7 29.1 + - - -
73K ARG* 3.0 19.3 + - + +
74K ASP 4.8 0.2 - - - -
75K PRO* 4.1 13.9 - - + -
81K ASN* 5.1 0.9 - - - +
109K LEU* 3.4 32.3 - - + -
112K LEU* 4.1 13.5 - - + -
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Residues in contact with VAL 8 (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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7K ILE* 1.3 73.9 - - - +
9K SER* 1.3 67.6 + - - +
32K THR* 2.8 16.8 + - + +
33K ASP 4.2 4.0 - - - +
34K GLU* 3.6 44.2 - - + +
71K ILE* 3.2 22.0 - - - +
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Residues in contact with SER 9 (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 VAL* 1.3 88.0 - - - +
10K VAL* 1.3 65.9 + - - +
11K GLU* 5.7 2.8 + - - +
30K LYS 4.4 1.1 + - - -
31K VAL* 3.5 9.2 - - - +
32K THR* 3.0 46.6 + - - +
71K ILE* 3.5 6.2 - - - +
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Residues in contact with VAL 10 (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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7K ILE* 4.5 0.4 - - + -
9K SER* 1.3 82.2 - - - +
11K GLU* 1.3 65.6 + - - +
12K PHE* 3.8 27.4 - - + -
29K VAL* 4.4 6.1 - - + -
30K LYS 3.5 4.7 - - - +
31K VAL* 4.1 13.9 - - + -
67K LYS* 3.0 47.7 + - + +
70K VAL* 3.7 30.5 - - + -
71K ILE* 3.9 9.3 - - + +
105K ILE* 4.2 13.7 - - + -
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Residues in contact with GLU 11 (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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9K SER* 5.7 2.8 + - - +
10K VAL* 1.3 76.5 - - - +
12K PHE* 1.3 68.1 + - - +
13K ILE* 3.8 28.2 + - + +
28K ILE 3.3 4.9 - - - +
29K VAL* 3.4 2.6 - - - -
30K LYS* 2.9 50.7 + - + +
67K LYS* 4.6 3.4 - - - +
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Residues in contact with PHE 12 (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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10K VAL* 3.8 22.4 + - + -
11K GLU* 1.3 80.4 - - - +
13K ILE* 1.3 61.7 + - - +
14K PRO* 3.3 11.4 - - - +
27K VAL* 3.9 20.6 - - + -
28K ILE 3.5 3.6 - - - -
29K VAL* 3.9 16.4 - - + -
43K ALA* 4.3 6.1 - - + -
50K MET* 3.7 22.2 - - + -
51K LYS* 3.6 19.8 - - + +
54K SER* 3.5 34.8 + - - +
55K GLU* 5.0 3.0 + - - +
66K ILE* 5.0 2.2 - - + -
67K LYS* 4.6 3.0 - - - +
101K ALA* 3.7 42.4 - - + -
105K ILE* 3.8 16.2 - - + -
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Residues in contact with ILE 13 (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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11K GLU* 4.1 31.4 - - + +
12K PHE* 1.3 75.3 - - - +
14K PRO* 1.3 66.3 - - + +
15K VAL* 3.4 9.0 - - + +
27K VAL* 4.0 2.8 - - - +
28K ILE* 2.8 46.9 + - + +
30K LYS* 4.3 16.4 - - + -
378K VAL* 5.0 2.9 - - + -
382K THR* 3.8 29.8 - - + -
386K PHE* 4.0 28.7 - - + -
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Residues in contact with PRO 14 (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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12K PHE 3.3 10.5 - - - +
13K ILE* 1.3 86.8 - - + +
15K VAL* 1.3 62.0 + - - +
16K ASN* 4.1 3.7 + - - +
26K THR 3.9 5.8 - - - +
27K VAL* 4.6 2.9 - - + -
47K PRO* 3.6 30.5 - - + +
48K GLU* 3.6 25.1 - - - +
51K LYS* 3.6 27.1 - - + -
382K THR* 3.8 16.6 - - - +
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Residues in contact with VAL 15 (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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13K ILE* 3.4 15.5 - - + +
14K PRO* 1.3 80.7 - - - +
16K ASN* 1.3 62.2 + - - +
17K VAL* 5.1 0.7 - - + -
24K GLU 3.9 0.2 - - - +
25K ASN* 3.2 24.8 - - - +
26K THR* 3.1 24.2 + - + +
28K ILE* 3.7 28.9 - - + -
47K PRO* 4.4 0.6 - - - +
345K LEU* 4.2 25.6 - - + -
349K LEU* 5.0 6.3 - - + -
378K VAL* 5.1 0.9 - - + -
381K VAL* 4.1 23.8 - - + -
382K THR* 4.6 7.4 - - + +
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Residues in contact with ASN 16 (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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14K PRO* 4.1 1.6 - - - +
15K VAL* 1.3 74.3 - - - +
17K VAL* 1.3 70.2 + - - +
18K ALA* 4.0 3.0 + - + +
23K SER* 5.5 4.7 - - - -
24K GLU 3.9 1.7 - - - +
25K ASN* 3.9 16.5 + - - +
47K PRO* 3.8 33.3 - - - +
48K GLU* 5.0 12.1 + - - +
381K VAL* 4.6 17.6 + - - +
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Residues in contact with VAL 17 (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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15K VAL* 5.1 1.6 - - + -
16K ASN* 1.3 80.9 + - - +
18K ALA* 1.3 68.8 - - - +
23K SER* 4.3 8.3 + - - -
24K GLU* 3.1 36.9 + - + +
344K THR* 4.1 24.9 - - + +
345K LEU* 3.9 29.6 - - + -
377K PHE* 4.3 13.5 - - + -
381K VAL* 4.7 7.9 - - + -
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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