Contacts of the strand formed by residues 109 - 114 (chain K) in PDB entry 1VQ4
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 LEU 109 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K ALA 3.5 5.2 - - - +
22K ASP* 4.4 2.7 - - + -
96K VAL* 3.5 39.0 - - + -
104K PRO* 4.5 10.3 - - + -
106K GLY 6.1 0.7 - - - +
108K GLU* 1.3 75.3 - - - +
110K LYS* 1.3 65.0 + - - +
111K GLY 3.7 2.6 - - - +
113K ILE* 3.2 32.1 - - + -
124K VAL* 3.1 37.7 - - + +
127K ALA* 3.6 28.0 + - + +
128K ALA* 4.2 1.6 - - - -
129K THR* 3.2 22.9 + - - -
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Residues in contact with LYS 110 (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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20K CYS 5.2 2.8 + - - +
21K ALA* 3.5 29.1 + - - +
22K ASP* 3.6 34.4 + - - +
23K ASN* 4.6 7.6 - - - +
75K ARG* 5.0 1.1 + - - +
108K GLU* 3.7 3.8 + - + +
109K LEU* 1.3 73.4 - - - +
111K GLY* 1.3 74.0 + - - +
112K PRO 4.3 1.9 - - - +
113K ILE* 4.9 1.4 - - - +
129K THR* 5.2 0.7 - - - -
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Residues in contact with GLY 111 (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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75K ARG* 3.9 11.2 - - - -
109K LEU 3.7 5.2 - - - +
110K LYS* 1.3 89.2 - - - +
112K PRO* 1.3 75.7 - - - +
113K ILE* 4.3 3.5 - - - +
129K THR* 4.9 1.1 + - - -
130K MET* 4.1 23.5 + - - +
24U LYS 4.3 4.5 - - - -
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Residues in contact with PRO 112 (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 ALA* 5.9 0.2 - - - +
74K VAL* 3.7 0.9 - - - +
75K ARG* 3.2 39.8 + - - +
90K PHE* 4.7 0.4 - - + -
110K LYS 4.3 1.0 - - - +
111K GLY* 1.3 82.8 - - - +
113K ILE* 1.3 72.1 + - - +
130K MET* 3.8 15.9 - - + +
132K VAL* 4.1 11.0 - - + -
22U VAL* 3.8 26.9 - - + -
23U HIS 3.8 7.9 - - - +
24U LYS 3.2 18.6 - - - +
26U GLY* 3.8 19.1 - - - +
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Residues in contact with ILE 113 (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 ALA* 6.3 0.2 - - + -
74K VAL* 3.0 33.2 - - + -
75K ARG* 4.5 0.9 - - - -
90K PHE* 4.3 5.4 - - - -
96K VAL* 5.2 1.1 - - + -
109K LEU* 3.2 40.8 - - + -
110K LYS 4.9 2.0 - - - +
111K GLY 4.3 4.5 - - - +
112K PRO* 1.3 83.9 - - - +
114K ALA* 1.3 76.3 + - - +
117K VAL* 4.1 13.9 - - + -
118K ALA 5.7 0.2 - - - +
124K VAL* 4.8 3.6 - - + +
125K ALA* 6.0 3.6 - - - -
128K ALA* 3.6 18.2 - - + -
130K MET 3.2 11.3 + - - +
131K ILE* 3.5 7.2 - - + -
132K VAL* 2.9 26.2 + - - +
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Residues in contact with ALA 114 (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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49K LEU* 3.6 42.2 - - + -
74K VAL 3.5 5.6 + - - +
80K ILE* 5.2 0.7 - - + -
82K ARG* 4.8 0.9 - - - +
90K PHE* 3.7 16.2 - - + -
113K ILE* 1.3 90.3 - - - +
115K ARG* 1.3 64.8 + - - +
116K GLU* 3.8 11.2 - - + +
117K VAL* 3.3 11.0 + - + +
118K ALA* 4.1 2.1 + - - +
131K ILE* 4.6 1.6 - - - +
132K VAL 3.5 5.2 - - - -
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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