Contacts of the strand formed by residues 16 - 22 (chain K) in PDB entry 1F1H
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 PHE 16 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K VAL* 2.9 9.4 - - - +
15K LYS* 1.3 93.9 - - + +
17K VAL* 1.3 64.5 + - - +
32K THR* 3.6 22.4 - - + -
33K ILE 3.5 2.9 - - - -
34K PRO* 3.9 20.0 - - + -
35K ALA 3.8 1.3 - - - +
82K ASP* 4.0 7.6 - - + -
83K SER 3.1 4.2 + - - -
84K THR* 3.0 3.5 - - - -
85K LEU 2.8 23.0 + - - -
1493K MPD 2.9 32.1 - - + -
193L SER* 3.5 33.9 - - - -
196L CYS* 3.9 19.3 - - + -
197L LEU* 3.5 33.7 - - + -
209L HIS* 4.3 4.7 - + - -
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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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9K LEU* 4.1 20.9 - - + -
16K PHE* 1.3 79.3 - - - +
18K ASP* 1.3 62.1 + - - +
19K LEU* 3.5 26.6 + - + -
32K THR* 3.4 3.5 - - - -
33K ILE* 2.7 46.9 + - + +
35K ALA* 4.4 6.1 - - - -
38K VAL* 3.7 26.7 - - + -
42K PHE* 5.1 1.1 - - + -
85K LEU* 3.1 16.4 - - + +
87K ILE* 3.9 18.4 - - + -
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Residues in contact with ASP 18 (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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17K VAL* 1.3 70.3 - - - +
19K LEU* 1.3 66.2 + - - +
20K ARG* 2.7 35.8 + - - +
30K HIS* 2.8 28.9 - - - +
31K VAL 3.5 4.4 - - - +
32K THR* 2.6 28.1 + - + +
80K PHE* 4.1 8.5 - - + -
84K THR* 4.0 15.4 + - - +
85K LEU 2.7 10.9 + - - +
86K ILE* 3.4 12.5 - - + +
87K ILE 2.9 24.8 + - - -
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Residues in contact with LEU 19 (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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17K VAL* 3.5 25.7 + - + -
18K ASP* 1.3 71.3 - - - +
20K ARG* 1.3 59.7 + - - +
21K PHE* 4.5 3.1 + - - -
30K HIS* 3.1 6.1 - - - -
31K VAL* 2.8 55.0 + - + +
33K ILE* 4.4 25.4 - - + -
42K PHE* 4.1 29.2 - - + -
47K LYS* 5.2 7.6 - - + -
67K LEU* 4.5 12.3 - - + -
87K ILE* 3.5 13.7 - - + +
89K CYS* 3.8 20.6 - - - -
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Residues in contact with ARG 20 (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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18K ASP* 2.7 27.8 + - - +
19K LEU* 1.3 78.6 - - - +
21K PHE* 1.3 64.0 + - - +
28K GLU* 3.1 31.6 + - + +
29K GLN 3.2 11.4 - - - +
30K HIS* 3.8 0.4 - - + -
77K ASP* 2.9 23.8 + - - -
80K PHE* 3.4 10.3 - - - -
86K ILE* 3.5 42.4 - - + +
87K ILE 3.0 8.4 + - - +
88K ARG* 3.3 13.1 - - - +
89K CYS* 2.7 33.0 + - - +
202K MET* 5.1 0.6 - - - +
240K TYR* 3.4 37.1 + - - -
182L VAL* 4.1 10.3 - - - +
183L PRO* 5.2 0.4 - - - +
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Residues in contact with PHE 21 (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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19K LEU 4.7 2.5 - - - -
20K ARG* 1.3 78.9 - - - +
22K THR* 1.3 63.6 + - - +
23K ASP* 5.0 0.7 - - - -
28K GLU* 3.3 5.5 - - - +
29K GLN* 2.5 69.8 + - + +
30K HIS* 4.7 2.2 - - - -
31K VAL* 5.2 1.3 - - + -
49K PHE* 4.3 16.6 - + - -
54K ILE* 4.5 9.0 - - + -
57K TRP* 3.7 35.9 - + - -
67K LEU* 3.7 29.2 - - + -
88K ARG* 5.2 6.1 - - - +
89K CYS 4.0 14.6 - - - +
91K ILE* 3.9 13.9 - - + -
103K ASP* 6.0 0.9 - - - +
180L PHE* 4.1 22.4 - + - -
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Residues in contact with THR 22 (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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21K PHE* 1.3 81.1 + - - +
23K ASP* 1.3 77.3 + - - +
26K GLY* 3.5 28.0 - - - -
27K LYS 3.6 2.9 - - - -
28K GLU* 4.3 2.1 - - - +
57K TRP* 3.6 9.0 - - - -
88K ARG* 4.9 2.1 + - - -
103K ASP* 4.7 2.5 + - - +
104K PRO* 3.6 18.7 - - + +
105K ARG* 5.9 2.7 - - - +
236K GLN* 2.8 24.1 + - - +
366K ASN* 4.1 7.0 - - - +
368K TYR* 3.4 32.2 + - + -
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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