Contacts of the strand formed by residues 108 - 112 (chain A) in PDB entry 5N4D
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 VAL 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.3 4.0 - - - -
99A TYR 2.9 37.3 + - - +
104A GLN* 4.0 17.3 - - - +
106A GLN 4.1 0.2 - - - +
107A SER* 1.3 76.8 - - - +
109A LEU* 1.3 64.3 + - - +
110A TYR* 3.5 27.3 + - + -
130A VAL* 3.8 25.1 - - + -
132A PHE 3.7 10.8 - - - +
133A ASP* 3.5 30.1 - - + +
134A PRO* 4.1 0.2 - - - -
135A ASN* 3.8 9.2 - - - +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.4 7.4 - - + -
97A TRP* 3.6 30.1 - - - +
98A PHE* 3.8 35.3 - - + -
107A SER 4.2 0.4 + - - -
108A VAL* 1.3 71.8 - - - +
110A TYR* 1.3 55.8 + - - +
130A VAL 3.9 0.3 - - - -
131A PHE* 2.8 40.3 + - + -
132A PHE* 2.8 31.5 + - + +
148A CYS* 4.9 0.4 - - - -
150A PHE* 3.8 17.9 - - + -
157A PHE* 3.5 37.9 - - + -
24C ILE* 4.5 5.8 - - + -
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Residues in contact with TYR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A TYR* 3.1 12.8 - - - +
97A TRP* 2.8 56.9 + + + +
99A TYR* 4.0 29.2 - + + -
101A ARG* 5.9 2.1 - - - +
108A VAL* 3.6 35.7 - - + -
109A LEU* 1.3 77.2 - - - +
111A ARG* 1.3 59.8 + - - +
124A ASP* 3.9 14.6 - - + -
125A ASP* 2.7 33.0 + - - -
128A GLY* 3.7 21.1 - - - -
129A ASP* 3.4 17.7 - - - -
130A VAL* 3.7 16.9 - - + +
131A PHE* 4.5 0.4 - - - -
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASP* 4.2 3.4 + - - +
94A HIS* 3.1 41.5 + - + -
95A TRP 3.4 4.0 - - - -
96A TYR* 3.4 44.7 + - + -
97A TRP* 4.0 3.4 - - - -
110A TYR* 1.3 74.5 - - - +
112A SER* 1.3 86.1 + - - +
113A LYS* 4.4 5.5 + - - +
128A GLY* 3.2 0.2 - - - -
129A ASP* 2.9 45.0 + - + +
130A VAL 5.5 0.4 - - - -
131A PHE* 4.1 11.2 - - + -
176A THR 5.1 7.5 + - - -
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A HIS* 2.8 26.2 + - - -
95A TRP* 2.8 40.5 + - - +
97A TRP* 3.5 5.0 - - - -
111A ARG* 1.3 82.5 + - - +
113A LYS* 1.3 60.8 + - - +
114A GLU 2.7 25.9 + - - -
116A ALA 4.3 1.1 - - - -
118A PRO* 4.0 24.0 - - - -
127A VAL 3.5 7.6 - - - -
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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