Contacts of the strand formed by residues 97 - 102 (chain F) in PDB entry 3M4D
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 97 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 4.0 15.9 + - - -
90F LEU* 4.1 1.6 - - - -
95F VAL 3.7 9.2 - - - +
96F ALA* 1.3 80.2 - - - +
98F ILE* 1.3 70.0 + - - +
162F ASP* 3.1 32.5 + - + +
163F LYS* 4.4 3.4 - - - +
232F ILE* 3.2 8.3 - - - -
233F THR* 2.9 40.4 + - - +
26G VAL* 3.3 39.7 + - + +
27G THR* 5.1 0.6 - - - +
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F LEU* 4.3 4.9 - - + +
90F LEU* 4.2 11.2 - - + -
97F GLN* 1.3 72.2 - - - +
99F SER* 1.3 60.3 + - - +
100F ASP 4.3 2.2 - - - +
101F TYR* 3.9 28.7 - - + -
161F THR 3.6 15.0 - - - +
162F ASP* 2.9 13.6 + - - +
163F LYS 3.3 5.8 - - - +
164F LYS* 3.1 47.3 - - - +
165F VAL* 3.5 15.9 - - + +
230F THR* 4.4 10.5 - - + -
231F VAL 3.7 8.5 - - - +
232F ILE* 4.5 5.2 - - + +
245F ILE* 6.1 1.1 - - + -
26G VAL* 3.7 9.4 - - - +
35G HIS* 2.9 20.7 + - - -
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Residues in contact with SER 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F GLN 3.3 0.6 + - - -
98F ILE* 1.3 75.0 - - - +
100F ASP* 1.3 60.5 + - - +
101F TYR* 5.0 0.5 - - - -
231F VAL* 2.7 19.8 + - - +
233F THR* 3.5 25.4 - - - +
24G ASP* 2.5 30.9 + - - -
26G VAL* 3.8 7.2 - - - -
35G HIS* 3.6 13.1 - - - -
37G LYS* 2.8 32.1 + - - +
59G GLY* 5.3 1.2 + - - -
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Residues in contact with ASP 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 3.6 16.9 - - + +
6E ASN* 3.9 2.9 - - - +
98F ILE* 3.9 0.5 - - - +
99F SER* 1.3 81.8 - - - +
101F TYR* 1.3 95.7 + - - +
104F ARG* 2.9 26.2 + - - -
230F THR* 3.7 3.3 - - - +
231F VAL* 2.8 41.9 + - + +
37G LYS* 3.9 10.1 + - - +
58G LYS* 2.8 33.7 + - - +
59G GLY 5.7 1.2 + - - -
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Residues in contact with TYR 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 4.5 3.1 - - - +
98F ILE* 3.9 14.8 - - + -
100F ASP* 1.3 98.1 + - - +
102F TYR* 1.3 65.2 + - - +
103F PRO 4.4 0.2 - - - -
104F ARG* 3.0 33.1 + - - +
157F LEU* 3.7 18.8 - - + -
160F PRO* 3.5 15.6 - - + +
165F VAL* 3.9 14.4 - - + -
167F TRP* 3.8 18.2 - - + -
229F ALA 3.1 14.1 - - - +
230F THR* 4.7 1.3 - - - -
231F VAL 4.8 0.2 - - - +
35G HIS* 2.6 39.7 + + - -
59G GLY* 3.1 11.1 - - - -
60G THR* 2.6 36.8 - - + +
225G SER* 4.2 3.4 - - - -
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Residues in contact with TYR 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ALA 4.2 15.9 - - - +
4E ASP* 3.5 45.1 + - + -
5E ILE* 4.3 13.5 - - + -
101F TYR* 1.3 75.5 - - - +
103F PRO* 1.3 88.7 - - + +
104F ARG* 3.6 26.2 - - + -
167F TRP* 3.8 2.7 - - - -
227F ASP 4.5 0.3 - - - +
228F PHE* 3.6 1.2 - - - -
229F ALA* 2.9 39.6 + - + +
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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