Contacts of the strand formed by residues 116 - 124 (chain A) in PDB entry 5FL6
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 ALA 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A HIS 3.2 15.3 - - - +
97A TRP* 4.0 12.1 - - + -
105A SER* 3.8 11.1 - - - +
114A PHE* 3.2 1.1 + - - +
115A PRO* 1.3 79.6 - - - +
117A GLU* 1.3 63.7 + - - +
146A PHE* 3.6 5.0 - - - +
147A LEU* 2.8 47.5 + - + +
224A LEU* 4.4 7.9 - - + -
227A LEU* 4.1 8.5 - - + -
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Residues in contact with GLU 117 (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 4.1 0.2 - - - +
95A LEU* 3.3 7.5 - - - +
96A HIS* 2.8 38.6 + - + +
105A SER* 3.5 13.6 - - - -
106A GLU* 2.8 28.1 + - - +
107A HIS* 2.8 33.5 + - - -
116A ALA* 1.3 76.5 - - - +
118A ILE* 1.3 62.1 - - - +
119A HIS* 2.7 34.5 + - + +
144A ALA* 3.6 6.3 - - - +
145A ALA 3.3 18.6 - - - +
146A PHE* 3.5 11.2 - - + -
147A LEU* 4.3 3.1 - - - -
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Residues in contact with ILE 118 (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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93A LEU* 4.0 24.9 - - + -
94A HIS 3.5 10.5 - - - +
95A LEU* 3.6 14.6 - - + -
117A GLU* 1.3 70.6 - - - +
119A HIS* 1.3 84.8 + - - +
120A VAL* 4.3 8.5 - - + -
143A LEU 3.6 0.6 - - - +
144A ALA* 3.2 2.4 - - - -
145A ALA* 2.9 53.8 + - + +
147A LEU* 4.0 5.3 - - + +
157A TYR* 3.4 27.1 - - + +
160A LEU* 6.4 0.2 - - + -
184A LEU* 3.9 21.5 - - + +
185A LEU* 4.0 10.1 - - + -
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Residues in contact with HIS 119 (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 GLN 4.1 0.2 - - - +
93A LEU* 3.1 5.5 - - - +
94A HIS* 2.9 48.4 + - + +
96A HIS* 3.2 11.1 + + - -
106A GLU* 3.2 23.6 - - + -
107A HIS* 5.1 0.2 - - - -
117A GLU* 2.7 31.6 + - + -
118A ILE* 1.3 87.0 - - - +
120A VAL* 1.3 62.6 + - - +
121A VAL 4.0 0.7 - - - -
142A VAL* 3.7 13.0 - - + -
143A LEU 3.3 2.7 - - - -
144A ALA* 3.7 12.1 - - + -
210A TRP* 3.6 18.3 - + - -
268A Y0R 3.5 2.4 + - - -
1260A ZN 2.2 32.9 - - - -
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Residues in contact with VAL 120 (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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53A PHE* 4.6 9.9 - - + -
74A LEU* 4.1 18.8 - - + -
90A ALA* 4.5 3.4 - - + -
92A GLN 3.6 9.4 - - - +
93A LEU* 4.0 14.8 - - + -
118A ILE* 4.3 7.9 - - + -
119A HIS* 1.3 75.3 - - - +
121A VAL* 1.3 59.9 + - - +
122A HIS* 3.0 31.8 + - + +
142A VAL* 3.3 2.3 - - - +
143A LEU* 2.9 39.1 + - + +
181A ILE* 5.3 1.3 - - + -
185A LEU* 3.9 33.9 - - + -
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Residues in contact with VAL 121 (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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90A ALA* 3.8 2.8 - - - +
91A LEU* 2.9 35.4 + - + +
92A GLN* 2.9 42.4 + - + +
94A HIS* 3.7 13.0 - - + -
119A HIS 4.6 0.2 - - - +
120A VAL* 1.3 74.1 - - - +
122A HIS* 1.3 68.8 + - - +
140A LEU* 5.0 12.3 - - + -
141A ALA 3.7 2.9 - - - -
142A VAL* 4.3 13.9 - - + -
199A LEU* 5.5 0.7 - - + -
268A Y0R 3.7 39.0 - - - +
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Residues in contact with HIS 122 (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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53A PHE* 3.8 8.5 - - - -
80A MET* 3.5 38.1 - - + +
88A TYR* 3.7 16.8 - - + -
89A ARG 3.2 7.9 - - - +
90A ALA* 3.4 31.4 - - + +
91A LEU* 4.4 3.4 - - - +
120A VAL* 3.0 45.1 + - + -
121A VAL* 1.3 73.2 - - - +
123A LEU* 1.3 59.7 + - - +
140A LEU* 3.3 13.9 - - - +
141A ALA 2.8 36.9 + - - +
143A LEU* 3.7 22.6 - - + +
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Residues in contact with LEU 123 (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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88A TYR* 3.3 3.3 - - - -
89A ARG* 2.9 36.8 + - + +
91A LEU* 3.8 26.0 - - + +
122A HIS* 1.3 74.5 - - - +
124A SER* 1.3 74.7 + - - +
127A PHE* 3.6 24.2 - - + +
128A ALA 3.9 9.2 - - - +
129A ARG* 3.8 21.5 - - - +
130A VAL* 3.9 7.0 - - + +
133A ALA* 3.4 33.4 - - + -
139A GLY 3.7 1.3 - - - +
140A LEU* 3.9 7.6 - - + -
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Residues in contact with SER 124 (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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87A GLU 3.7 4.1 + - - -
88A TYR* 3.3 16.3 - - - -
123A LEU* 1.3 75.8 - - - +
125A THR* 1.3 59.6 + - - +
126A ALA* 3.0 28.8 + - - +
127A PHE* 3.0 31.0 + - - +
138A GLY 3.6 16.2 - - - -
139A GLY* 2.8 22.3 + - - -
137B PRO* 4.0 10.8 - - - +
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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